@article {pmid41218045,
year = {2025},
author = {Kitsanayanyong, L and Chongprachavat, N and Rairat, T and Keetanon, A and Wimanhaemin, P and Chuchird, N},
title = {Exploring the gut microbiota of Pacific white shrimp (Litopenaeus vannamei) suffering pale shrimp disease.},
journal = {PloS one},
volume = {20},
number = {11},
pages = {e0336700},
doi = {10.1371/journal.pone.0336700},
pmid = {41218045},
issn = {1932-6203},
abstract = {Pale shrimp disease is an emerging threat in Thailand, characterized by pale body coloration in Pacific white shrimp (Litopenaeus vannamei). Although the etiology had been identified as Photobacterium damselae subsp. damselae, the disease effects on gut microbiome remain poorly understood. This study investigated changes in the gut microbiota of Pacific white shrimp suffering from pale shrimp disease (diseased group) compared to disease-free shrimp (healthy group) collected from Surat Thani Province, Thailand. DNA extracted from the intestinal samples was subjected to 16S rRNA metagenomic sequencing, followed by taxonomic identification, diversity analyses, and functional prediction of the metabolic pathways. Despite a limited number of biological replicates, the occurrence of pale shrimp disease was able to reveal alterations in intestinal microbial composition, diversities, and functional features compared to the healthy shrimp. In most cases, the intestinal microbiota of the diseased shrimp were dominated by only 2 genera of bacteria, i.e., Photobacterium (54.63-70.53%) and Vibrio (24.94-26.12%), which together accounted for 79.58-95.47% of the total bacterial community. α-diversity, as indicated by the observed features, Shannon, and Simpson indices, was significantly decreased, and dominance was significantly increased in the diseased shrimp compared to healthy shrimp. Likewise, β-diversity was significantly different between groups; PCoA of un-weighted and weighted UniFrac clearly distinguished intestinal microbiota of the shrimp into 2 clusters, and ANOSIM of these data revealed statistical differences between groups, suggesting different microbiota communities between healthy and diseased shrimp. Moreover, diseased shrimp had significantly higher predicted functional features associated with bacterial virulence factors and antibacterial resistance. These exploratory findings suggest an association among pale shrimp disease, gut microbiota dysbiosis, and the proliferation of opportunistic taxa, particularly Photobacterium.},
}

@article {pmid41217799,
year = {2025},
author = {Ponomarenko, IG and Ponomarenko, GN},
title = {[Connective tissue diseases: development predictors, multimorbidity variants, physical treatment methods. (Literature review)].},
journal = {Voprosy kurortologii, fizioterapii, i lechebnoi fizicheskoi kultury},
volume = {102},
number = {5},
pages = {56-62},
doi = {10.17116/kurort202510205156},
pmid = {41217799},
issn = {0042-8787},
abstract = {UNLABELLED: Connective tissue diseases, such as systemic lupus erythematosus, systemic scleroderma and dermatomyositis are heterogeneous autoimmune diseases with damage to the skin, vessels and internal organs, immune dysregulation, fibrosis. The relevance of their study is due to high multimorbidity, including cardiovascular, oncological and neuropsychiatric complications (pulmonary hypertension develops in 30-40% of patients with scleroderma, paraneoplastic syndromes are recorded in 40% of patients with dermatomyositis). Increase in knowledge of genetic and epigenetic factors triggering debut of connective tissue diseases emphasizes the need for an interdisciplinary approach and personalization of therapy.

OBJECTIVE: To analyze the modern data on pathogenesis, genetic predictors, clinical complications and comorbid conditions, methods of treatment of the connective tissue diseases, as well as to evaluate the promising research directions for improving diagnosis and therapy.

MATERIAL AND METHODS: A review of scientific publications and clinical studies presented in international abstract databases for the period from 2013 to 2025 involving more than 700 thousand patients was carried out. Data on genetic biomarkers, epidemiological factors, effectiveness of physical methods of treatment of the connective tissue diseases and innovative approaches were systematized.

RESULTS: Key genetic (polymorphisms of HLA class II, TRAF1-C5, TNFSF4, antibodies to MDA5) and epigenetic risk factors (insolation, smoking, vitamin D deficiency) of the connective tissue diseases have been identified. Effectiveness of physical therapy for improvement of the function of joints and lungs, phototherapy for correction of skin manifestations has been proven. Autologous stem cell transplantation has shown effectiveness in refractory forms. Personalization of biomarker-based therapy improves patients' quality of life. The main challenges have been established: resistance to therapy, risk of infections during immunosuppression. The investigation of gut microbiome and development of targeted drugs inhibiting TGF-β and interleukin-6 have been recognized as promising directions.

CONCLUSION: Connective tissue diseases require early diagnosis, interdisciplinary strategy and integration of pharmacological and non-drug methods. Physical treatment methods demonstrate proven effectiveness in the context of a comprehensive approach to therapy. Physical therapy with a high level of evidence (I, A) improves the function of joints and lungs, as well as contributes to the reduction of fibrosis severity. UVA-1 phototherapy is a method of choice for improving the skin elasticity in scleroderma and skin forms of the connective tissue diseases by inhibiting TGF-β and collagen synthesis. Ultrasound therapy in combination with hyaluronidase, high-intensity dye laser therapy are indicated for reduction of the vascular disorders in tissues. Cryotherapy (whole-body and local), electrophoresis with corticosteroids have a local anti-inflammatory effect, complement the range of non-drug interventions, improving the quality of life of patients, but require individualization of parameters. Personalization of treatment based on genetic markers, as well as the introduction of innovative methods (targeted therapy) can reduce the risk of complications, but problems of resistance and iatrogenic effects remain. Further research should be aimed at the study of the role of microbiome and development of pathogenetically substantiated drugs.},
}

@article {pmid41217655,
year = {2025},
author = {Mohammadi Dehcheshmeh, M and Grant, L and Ebrahimie, E and Khabiri, A and Hemmatzadeh, F and Shipstone, M and Trott, DJ},
title = {Oral probiotic and postbiotic supplementation enhances the abundance of Lactobacillus acidophilus, Lactobacillus johnsonii, and Limosilactobacillus reuteri in both canine skin and gastrointestinal microbiota: insights from long-read 16S rRNA gene sequencing.},
journal = {Veterinary research communications},
volume = {50},
number = {1},
pages = {29},
pmid = {41217655},
issn = {1573-7446},
abstract = {Oral daily probiotic and postbiotic supplementation (ODPPS) is a promising strategy for canine skin and gut health. Despite growing interest, the effects of ODPPS on the composition of the canine gut and skin microbiota remain largely unexplored. The advent of full-length 16S rRNA gene sequencing has opened new avenues in microbiome research, significantly enhancing the accuracy and completeness of microbial community profiling. This study employed PacBio long-read sequencing to profile longitudinal changes in canine fecal microbiota composition during ODPPS. Then, we evaluated the parallel dynamics between fecal and skin microbiota responses to ODPPS, addressing a critical gap in understanding systemic microbiome interactions in dogs. By Day 90, fecal microbiota composition shifted significantly (PERMANOVA p = 0.05), with increased beneficial bacteria by Day 30 and further by Day 90. In both axillae and fecal microbiota, ODPPS supplementation increased the relative abundance of beneficial species including Lactobacillus acidophilus, Lactobacillus johnsonii, and Limosilactobacillus reuteri. A significant positive Pearson correlation was found between the relative abundances of these bacteria in the skin and fecal microbiota (p = 0.05), suggesting a coordinated microbial response across body sites. The results highlight the significance of Lactobacillus acidophilus as a core probiotic strain, demonstrating exceptional capacity for colonisation and establishment in both the gastrointestinal and skin niches of dogs. These findings show the systemic influence of ODPPS in shaping microbial communities across both sites and support its use to promote overall canine health. Collectively, our results offer robust evidence for the dual benefits of daily oral ODPPS on both skin and gut microbiota.},
}

@article {pmid41217383,
year = {2025},
author = {Kelchtermans, J and Phinizy, P and Piccione, J and McGrath-Morrow, SA},
title = {Lower Respiratory Tract Bacterial Profiles Are Associated With Respiratory Severity and Bronchopulmonary Dysplasia in Neonates.},
journal = {Pediatric pulmonology},
volume = {60},
number = {11},
pages = {e71364},
doi = {10.1002/ppul.71364},
pmid = {41217383},
issn = {1099-0496},
support = {//This study was supported by the Parker B. Francis Fellowship Program. The study was funded by an Institute Development Fund and a K-readiness pilot grant from The Children's Hospital of Philadelphia. Research reported in this publication was supported by the National Institute of Environmental Health Sciences of the National Institutes of Health under grant number P30ES013508 and by the National Heart, Lung, and Blood Institute under grant number R01HL169859 and K08HL173625. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health./ ; },
abstract = {INTRODUCTION: Bronchopulmonary dysplasia (BPD) is a major complication of prematurity, marked by heterogeneous pulmonary phenotypes and variable clinical outcomes. The airway microbiome may influence disease severity and progression, yet quantitative associations between airway pathogens and clinically relevant outcomes remain poorly understood.

METHODS: We conducted a retrospective analysis of 204 neonates who underwent flexible bronchoscopy with quantitative bronchoalveolar lavage (BAL) cultures in the NICU at the Children's Hospital of Philadelphia. Cultures yielding ≥ 10,000 colony-forming units per milliliter for a single bacterial species were classified as positive. Respiratory severity score (RSS), calculated as the product of mean airway pressure and fraction of inspired oxygen, served as the primary indicator of respiratory status. Linear, logistic, and negative binomial regression models were used to assess associations between bacterial species and clinical outcomes, adjusted for sex and race, with standard errors clustered at the patient level.

RESULTS: No bacterial species were significantly associated with RSS after correction for multiple testing. Klebsiella pneumoniae was associated with a diagnosis of BPD (adjusted p = 0.026), but no organisms were significantly associated with prolonged time to extubation. In secondary analyses, the presence of several organisms was significantly associated with higher MAP, including K. pneumoniae (β = 2.66, FDR-adjusted p = 0.014).

CONCLUSIONS: Multiple bacterial species identified on quantitative BAL culture were associated with higher mean airway pressure, and K. pneumoniae was additionally associated with BPD diagnosis. These findings support the potential utility of quantitative microbiologic data in risk stratification and management of neonatal respiratory disease.},
}

@article {pmid41217190,
year = {2025},
author = {Su, N and Han, S and Li, Z and Ling, X and Kong, L and Song, D},
title = {Sargassum fusiforme polysaccharides modulate gut microbiota and metabolites to regulate hyperlipidemia in mice fed a high-fat diet.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0144525},
doi = {10.1128/aem.01445-25},
pmid = {41217190},
issn = {1098-5336},
abstract = {UNLABELLED: Hyperlipidemia complications caused by obesity are a hot issue threatening human health worldwide, and there is an urgent need to explore low-toxicity health foods for intervention. Sargassum fusiforme polysaccharides (SFPS) display cholesterol-lowering properties, but the underlying mechanism has not been elucidated. This study investigates the mechanisms by exploring changes in gut microbiota composition, gene expression, and metabolites in mice fed a high-fat diet after intervention with S. fusiforme fucoidan (SFF) and SFPS through 16S rRNA sequencing, transcriptomics, and non-targeted metabolomics. The experimental findings indicated that SFPS markedly enhanced the abundance of Akkermansia while concurrently reducing the levels of Actinobacteria, Erysipelotrichaceae, Bifidobacteriaceae, and Peptostreptococcaceae. This was achieved by upregulating the expression of Mt1, Prlr, and slc25a21 and downregulating SREBP-1, thereby inhibiting the cholesterol metabolism pathway. These changes resulted in increased hepatic production and fecal excretion of bile acids and reduced hepatic cholesterol. Our results shed light on the mechanisms behind the cholesterol- and lipid-lowering effects of SFPS, suggesting its potential as a therapeutic agent for hypercholesterolemia.

IMPORTANCE: Obesity and its associated metabolic disorders pose a global health challenge, necessitating safe and scalable interventions. This study demonstrated that polysaccharides from Sargassum fusiforme (SFPS), extracted via a novel non-alcoholic precipitation method, effectively ameliorate high-fat diet (HFD)-induced obesity by remodeling gut microbiota and restoring metabolic homeostasis. Integrating multi-omics approaches, we reveal that SFPS enriches beneficial taxa like Akkermansia while suppressing obesity-linked bacteria like Actinobacteria, Erysipelotrichaceae, and Bifidobacteriaceae; modulates cholesterol metabolism through gene regulation (e.g., downregulating Srebf1 and upregulating Mt1); and enhances bile acid excretion. Notably, SFPS exhibits efficacy comparable with the well-studied fucoidan (SFF); however, its cost-effective extraction method offers superior scalability for functional food development. These findings underscore the potential of SFPS as a prebiotic agent targeting the gut-liver axis, providing mechanistic insights into natural product-based strategies for metabolic disease management. This work advances our understanding of how polysaccharides interact with the host microbiome and metabolism, advancing dietary interventions for obesity management one step further.},
}

@article {pmid41217181,
year = {2025},
author = {Weinberger, V and Neumann, C and Kumpitsch, C and Duller, S and Shinde, T and Mantaj, P and Schmidberger, L and Zurabishvili, T and Halmer, I and Cecovini, M and Vrbancic, S and Pepper, K and Schmon, E and Wenninger, J and Kamolz, L-P and Sendlhofer, G and Koskinen, K and Moissl-Eichinger, C and Mahnert, A},
title = {Colonizing the clinic: tracking bacterial succession and longitudinal dynamics in five new hospital departments over an entire year.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0217825},
doi = {10.1128/spectrum.02178-25},
pmid = {41217181},
issn = {2165-0497},
abstract = {The development of hospital-associated microbial communities over time remains poorly characterized, particularly in terms of how microbial populations dynamically respond to changes in building function, the integration of molecular and cultivation-based data, and the early identification of intervention points for flexible, adaptive microbial control strategies. In this longitudinal study, we investigated microbiome dynamics across five newly built departments at the University Hospital of Graz, Austria, over one year. Surface samples were collected at seven time points: before and after hospital operation started. Alpha and beta diversity analyses revealed a distinct two-phase microbial transition, marked by an initial disruption followed by a gradual homogenization of microbial communities. The strongest driver of community change was the arrival of patients, which led to a significant shift in both diversity and taxonomic composition. While early time points were dominated by environmental taxa such as Acinetobacter and Pseudomonas, human-associated genera like Staphylococcus and Corynebacterium became more prevalent over time, particularly on frequently touched surfaces. Department-specific and surface-specific microbial signatures were observed, with outpatient and transplant departments showing more variability than surgical and intensive care units (ICUs). Propidium monoazide treatment indicated that Pseudomonas and Acinetobacter may persist as viable community members, whereas Staphylococcus and Corynebacterium likely reflect frequent human deposition. Cultivation data supported these findings, showing episodic contamination primarily linked to human contact. Phenotypic predictions revealed a decline in aerobic, Gram-negative, and potentially pathogenic bacteria over time, although these trends were less pronounced in the ICU. Together, our findings reveal a longitudinal homogenization of hospital microbiomes driven by human activity and highlight key taxa and surfaces that warrant targeted monitoring to improve hygiene protocols and infection control strategies.IMPORTANCEThis study provides crucial insights into how hospital environments transform microbially after new departments open, a process poorly understood until now. We reveal a two-phase microbial shift, starting with environmental bacteria like Acinetobacter and Pseudomonas before the hospital opens, then rapidly transitioning to human-associated microbes such as Staphylococcus and Corynebacterium once patients and staff arrive. Our findings highlight that human activity is the strongest driver of these changes, especially on frequently touched surfaces. This work is vital for developing targeted and adaptive hygiene concepts, improving infection control, and ultimately making hospital environments safer for patients and staff by focusing on specific surfaces and microbial groups that warrant continuous monitoring.},
}

@article {pmid41217033,
year = {2025},
author = {Ye, Y and Ge, J and He, W and Zhan, P and Wang, D and Wang, P and Tian, H and Liu, J},
title = {Polyphenols of Ferula lehmanni Boiss. attenuate high-fat diet-induced liver injury by regulating lipid synthesis and remodeling the gut microbiota.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo03998c},
pmid = {41217033},
issn = {2042-650X},
abstract = {High-fat diet (HFD)-induced liver injury, characterized by hepatic steatosis, inflammation, and oxidative stress, represents a significant global health challenge. Ferula lehmannii Boiss. (FLB), an edible and medicinal plant, is rich in polyphenols and has hepatoprotective effects, but the gut microbiota-mediated mechanism remains unclear. This study elucidates the protective effects of FLB polyphenols (FLBP) against HFD-induced liver injury via the gut microbiota. Chemical profiling and network pharmacology predicted FLBP's multitarget effects on lipid metabolism and inflammation. In vivo, FLBP attenuated hepatic steatosis by regulating lipogenic factors and energy metabolism, reducing oxidative stress and enhancing antioxidants. Gut microbiota analysis showed that FLBP restored gut microbial diversity, enriched beneficial bacteria abundance and promoted short-chain fatty acid (SCFA) production. Antibiotic-induced microbiota ablation abolished the hepatoprotective effects of FLBP, confirming the essential role of the gut microbiota. Collectively, our findings demonstrate that FLBP alleviates HFD-induced liver injury by regulating hepatic lipid synthesis and remodeling the gut microbiome, highlighting its potential as a dietary intervention for managing diet-related liver diseases.},
}

@article {pmid41216638,
year = {2025},
author = {Nakajima, Y and Okazaki, S and Tamura, M and Sato, S and Imai, K},
title = {Establishment of a coculture system for Porphyromonas gingivalis and head and neck squamous cell carcinoma using spheroid culture and LATS inhibition.},
journal = {FEBS open bio},
volume = {},
number = {},
pages = {},
doi = {10.1002/2211-5463.70154},
pmid = {41216638},
issn = {2211-5463},
support = {SATO-2023-6//Sato Fund/ ; a Nihon University Research Grant-in-Aid for Early//Nihon University/ ; //the research grant of Nihon University/ ; //Mishima Kaiun Memorial Foundation/ ; //NSK Nakanishi Foundation/ ; DRC(B)-2023-6//Dental Research Center, Nihon University School of Dentistry/ ; DRC(B)-2024-6//Dental Research Center, Nihon University School of Dentistry/ ; DRC(B)-2025-6//Dental Research Center, Nihon University School of Dentistry/ ; JP22K07157//Japan Science and Technology Agency/ ; JP23K27810//Japan Science and Technology Agency/ ; JP24K22196//Japan Science and Technology Agency/ ; },
abstract = {Porphyromonas gingivalis (Pg) is a periodontal pathogen that has been implicated in the development and progression of head and neck squamous cell carcinoma (HNSCC). However, studying its interaction with HNSCC in vitro is challenging because of the obligatory anaerobic nature of Pg. To overcome this limitation, we developed a coculture system that enables the viability of both HNSCC cells and Pg using spheroid culture combined with Hippo pathway inhibition via treatment with a LATS1/2 inhibitor. In spheroid cultures, many HNSCC cell lines failed to grow in a normal medium. However, stable growth of these cells was achieved through Hippo pathway inhibition, which maintained the cells in an undifferentiated state. Furthermore, the addition of Pg to HNSCC spheroids maintained Pg viability in three out of four HNSCC cell lines, even after 3 days. Hippo pathway inhibition further enhanced Pg survival within the spheroids, likely by suppressing the differentiation-induced expression of antimicrobial genes S100A8 and S100A9. Coculturing HNSCC cells with Pg did not promote spheroid growth but induced p38 activation, leading to increased expression of the proinflammatory cytokines IL-1α and IL-8. Database analysis using The Cancer Microbiome Atlas corroborated these findings, showing upregulation of p38 phosphorylation, IL-1α, and IL-8 in Porphyromonas-positive HNSCC samples. These findings suggest that the established coculture system is a representative model of the clinical properties of Pg-positive HNSCC and can serve as a valuable tool for investigating the long-term interactions between HNSCC and viable Pg.},
}

@article {pmid41216332,
year = {2025},
author = {Facciotti, F and Di Stefano, G and Maragno, P and Ferraro, C and Dridi, D and Somigliana, E and Viganò, P and Vercellini, P and Casalechi, M},
title = {Microbiome dysbiosis and endometriosis: a systematic scoping review of current literature and knowledge gaps.},
journal = {Human reproduction open},
volume = {2025},
number = {4},
pages = {hoaf061},
pmid = {41216332},
issn = {2399-3529},
abstract = {STUDY QUESTION: What is the evidence available concerning gut and reproductive tract microbiomes in patients with endometriosis and what are the methodological approaches employed in microbiome studies on endometriosis?

SUMMARY ANSWER: The taxonomic profiles exhibited pronounced heterogeneity within women with and also within women without endometriosis across reviewed studies for all the anatomical districts evaluated.

WHAT IS KNOWN ALREADY: Both human and animal studies support differences in the microbiome composition of individuals with and without endometriosis. Endometriosis onset occurs with variable symptoms and manifestations. The microbiome composition at different sites may contribute to this variability.

STUDY DESIGN SIZE DURATION: We used the scoping review methodology. Systematic searches of studies from the PubMed, EMBASE, and Web of Science databases published between 1 January 2016 and 1 November 2024 addressing endometriosis microbiome characterization in: (i) gut, (ii) vaginal fluid, (iii) cervical fluid, (iv) peritoneal fluid, (v) uterine fluid, (vi) ovarian cyst fluid, (vii) oropharyngeal fluid, and (viii) eutopic and (ix) ectopic tissues were performed using a combination of MeSH terms. References from relevant publications were systematically screened.

Results were reported in accordance with the PRISMA-ScR guidelines. Studies that did not report original data, not written in English or providing a review of the field were excluded. From the 2182 publications retrieved, 36 papers were selected and analyzed, focusing on sample characterization (patients, controls, tissues, and fluids) and methodologies used.

Sound evidence is lacking to support a specific gut dysbiosis profile in women with endometriosis. The largest metagenome study performed using shotgun sequencing and controlling for multiple hypotheses testing did not detect significant differences between women with and without the disease. For eutopic and ectopic tissue microbiomes, the literature is too scant to draw any conclusion. Some data suggest a possible enrichment of Streptococcus sp. in cervical fluid and of Pseudomonas sp. in peritoneal fluid and a depletion of Lachnospira sp. in stool/anal fluid of endometriosis patients. However, these findings may be explained by confounders or by intrinsic patient or population characteristics. We appraised the limitations of the studies and proposed suggestions for optimizing sequencing techniques and experimental designs.

The number of participants per study greatly varied and, with few exceptions, was typically low. Incomplete information on methodological approaches was broadly observed. The impact of participants' menstrual cycle phase, diet, and drug assumption was frequently not considered.

Standardization of research protocols to allow reproducibility is required, as well as collaborations to harmonize data analysis, interpretation, and, more importantly, health outcome prediction or improvement.

The review was funded by the Italian Ministry of Health: RF-2019-12369460, and Current Research IRCCS. P.Vi. serves as co-editor in Chief of Journal of Endometriosis and Uterine Disorders. E.S. serves as Editor in Chief of Human Reproduction Open and discloses research grants from Ferring, Ibsa, Gedeon Richter, and Theramex, and honoraria from Ibsa and Gedeon Richter. P.Ve. serves as Associate Editor for Human Reproduction Open; is a member of the Editorial Board of the Journal of Obstetrics and Gynaecology Canada, of the Italian Journal of Obstetrics and Gynaecology, and of the International Editorial Board of Acta Obstetricia et Gynecologica Scandinavica; has received royalties from Wolters Kluwer for chapters on endometriosis management in the clinical decision support resource UpToDate; and maintains both a public and private gynecological practice. All other authors declare they have no conflict of interest.

REGISTRATION NUMBER: 10.17605/OSF.IO/X6HBT at https://osf.io/registries.},
}

@article {pmid41216323,
year = {2025},
author = {Shan, E and Yu, Z and Cong, X and Hou, C and Guo, X and Pang, L and Zhao, J and Wang, Q and Yuan, X},
title = {Gut microbial community plasticity as a climate shield mediating sea cucumber resilience to ocean acidification and warming.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf188},
pmid = {41216323},
issn = {2730-6151},
abstract = {Ocean acidification (OA) and ocean warming (OW) pose escalating threats to marine ecosystems, particularly to benthic organisms, such as sea cucumbers, that play pivotal roles in nutrient cycling and sediment health. Existing research mainly addresses sea cucumbers' physiological responses, overlooking gut microbial communities and metabolites in their stress adaptation. Herein, a mesocosm was constructed and analyzed by using integrated gut microbiome and metabolomics approaches to investigate the responses of sea cucumbers Apostichopus japonicus to OA and OW. Results revealed that microbial community plasticity underpins holobiont adaptation, with warming restructuring gut microbiota toward thermotolerant taxa, whereas acidification enriches alkalinity-modulating Rhodobacteraceae and Halioglobus sp. Metabolomic profiling identified 43 amino acid derivatives with significantly increased concentrations in OA and OW groups, including upregulated N-methyl-aspartic acid and γ-glutamyl peptides that stabilize macromolecules and enhance redox homeostasis. Conversely, antioxidative metabolites (e.g., ergothioneine, L-homocystine) are suppressed, reflecting trade-offs between energy allocation and stress protection. In OW group, the antioxidant synthesis pathway is shifted to energy metabolism related to heat tolerance, whereas in OA group, energy is preferentially used for alkalinity regulation pathways rather than oxidative stress defense. Changes in microbial community structure mechanistically explain the trends in metabolite concentrations, as the proliferation of Vibrio spp. in the OW group drives lysine catabolism, leading to a significant increase in L-saccharopine levels. Bacteroidetes reduction in the OA group correlates with L-homocystine downregulation, suggesting that pH-driven microbial interactions are disrupted. These findings demonstrate gut microbiota reshape community structure and metabolism to mitigate synergistic climate stress, emphasizing microbiome-mediated resilience in marine ecosystems amid global climate change.},
}

@article {pmid41216320,
year = {2025},
author = {González-Rosales, C and Rezaei Somee, M and Buck, M and Bertilsson, S and Mehrshad, M and Dopson, M},
title = {A global deep terrestrial biosphere core microbiome.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf176},
pmid = {41216320},
issn = {2730-6151},
abstract = {The deep biosphere encompasses life beneath the Earth's surface and constitutes a substantial portion of the planet's microbial biomass. This study analyzed nucleic acid datasets from low-carbon and low-energy deep terrestrial subsurface groundwaters across four continents and revealed four core global populations. These populations exhibited metabolic strategies and adaptations reflecting depth and environmental constraints. Erythrobacter featured heterotrophic metabolism; Thiobacillus demonstrated sulfur oxidation coupled to denitrification along with carbon and nitrogen fixation; Methanobacteriaceae were methanogenic autotrophs using the Wood-Ljungdahl pathway (WL); and Candidatus Desulforudis audaxviator functioned as a sulfate-reducer also encoding the WL pathway. Depth-related adaptations suggested heterotrophic dominance at shallower depths with increasing contributions from autotrophy with depth. Finally, comparative genomics revealed minimal evolutionary changes among these populations, suggesting functional conservation since diverging from their ancestral lineages. These findings underscore a global deep biosphere core community.},
}

@article {pmid41216319,
year = {2025},
author = {Bentzon-Tilia, M and Henriksen, NNSE and Schostag, MD and Andersen, AJC and Melchiorsen, J and Strube, ML and Gram, L},
title = {Autecology of an oscillating population of a novel host-associated Phaeobacter species proliferating in marine bryozoans.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf178},
pmid = {41216319},
issn = {2730-6151},
abstract = {Phaeobacter are marine alphaprotebacteria capable of producing a potent antibacterial compound, tropodithietic acid. Here we demonstrate that they are part of the microbiome of marine bryozoans where they during warmer months reach 10[5] CFU/g. The levels exhibited a bimodal fluctuation, in both bryozoans and seawater across seasons. However, the population of Phaeobacter sp. was already established in the bryozoans prior to the peak in seawater and did not accumulate as a function of filter feeding on phytoplankton biomass, suggesting that the seawater population is likely seeded from the bryozoan-associated Phaeobacter sp. population rather than the opposite. By comparing whole-genome sequences of more than 100 bryozoan-associated Phaeobacter isolates sampled over a 12-year period, we found that all belonged to the same novel species and no systematic genetic changes occurred within it over the 12 year sampling period despite the fact that the population oscillated from below the limit of detection and across five orders of magnitude to 5.2 Log10 CFU g[-1] bryozoan within individual years and hence were subject to drift. All isolates had the genetic capacity to produce tropodithietic acid (TDA) and the algicidal compounds, roseobacticides. The genes encoding the enzymes for TDA biosynthesis remained stable over time, indicating a conserved phenotype important in the ecophysiology of the bacteria. TDA biosynthetic genes were actively transcribed within the bryozoan host further corroborating the notion that the secondary metabolites of this novel host-associated Phaeobacter sp. may be central to its role within the bryozoan microbiome.},
}

@article {pmid41215794,
year = {2025},
author = {Onile-Ere, O and Name, PE and Tibiri, EB and Tiendrébéogo, F and Pita, J and Mohammed, IU and Nkere, CK and Oranusi, S and Eni, A},
title = {Dataset of rolling circle amplification (RCA) enriched metagenome of Cassava obtained through nanopore sequencing.},
journal = {Data in brief},
volume = {63},
number = {},
pages = {112204},
pmid = {41215794},
issn = {2352-3409},
abstract = {The dataset presented here was obtained by sequencing selected historic herbarium cassava samples collected across Nigeria. Total DNA was extracted from the samples using the CTAB method, after which the samples were enriched by Rolling Circle Amplification (RCA) and then sequenced on the MinION. The dataset consists of raw sequencing data in FASTQ format reflecting microbial diversity in cassava leaf samples. Taxonomic classification of the samples using the Kraken2 PlusPFP-16 database revealed 12 kingdoms, 36 phyla, 67 classes, 154 orders, 273 families, 524 genera, and 895 species across the dataset, with a substantial proportion (77.9%) of reads remaining unclassified following host removal. The data is beneficial for exploring the microbiome diversity of cassava leaves across Nigeria, as well as serving as a reference for future microbial discovery, given the large number of unidentified reads in the dataset.},
}

@article {pmid41215769,
year = {2025},
author = {Zhou, M and Lu, L and Xu, X and Zhou, Y and Fang, H and Wang, X and Li, D and Li, X and Hua, J and Liu, J and Li, Y and Jiang, L and Miao, Q and Wen, H and He, J and Yang, S},
title = {EUK nanozyme-loaded PL&GA coacervate droplets attenuate ulcerative colitis through restoring gut homeostasis and restricting intestinal cell ferroptosis.},
journal = {Materials today. Bio},
volume = {35},
number = {},
pages = {102466},
pmid = {41215769},
issn = {2590-0064},
abstract = {Ulcerative colitis (UC), a prevalent form of inflammatory bowel disease (IBD), manifests as chronic diarrhea, abdominal pain, and bloody mucoid stools. Current treatment approaches for UC are typically limited by inadequate targeted delivery, premature gastrointestinal degradation, and systemic off-target effects. To address these challenges, we engineered PL&GA@EUK, EUK-134 nanozymes encapsulated in polylysine (PL) and glycyrrhizic acid (GA) coacervate droplets. PL&GA@EUK exhibited potent superoxide dismutase- and catalase-mimetic activities, scavenging hydroxyl radicals and demonstrating anti-inflammatory efficacy in both in vivo and in vitro models. In mice with dextran sulfate sodium-induced colitis, oral administration of PL&GA@EUK for 14 days significantly ameliorated the disease activity index and colonic damage. By maintaining the integrity of the intestinal mucosal barrier and modulating redox homeostasis, it protects the intestinal epithelial cells against ferroptosis, ultimately attenuating colitis progression. 16S rDNA sequencing revealed that PL&GA@EUK significantly enriched beneficial commensals, while suppressing opportunistic pathogens. Metabolomic analysis further indicated that it modulates lipid peroxidation-associated metabolites by regulating the biosynthesis of polyunsaturated fatty acids. Crucially, PL&GA@EUK achieved enhanced colon-targeted delivery with minimal systemic toxicity, thereby overcoming the key limitations of conventional treatments. The multifaceted mechanism of PL&GA@EUK, involving reactive oxygen species scavenging, gut microbiome remodeling, and ferroptosis suppression, underscores its immense promise for the clinical management of IBD.},
}

@article {pmid41215695,
year = {2025},
author = {Siddiqui, R and Qaisar, R and Maciver, S and Khan, NA},
title = {Gut microbiome, stress and interventional strategies using hardy animals.},
journal = {Future science OA},
volume = {11},
number = {1},
pages = {2583020},
doi = {10.1080/20565623.2025.2583020},
pmid = {41215695},
issn = {2056-5623},
abstract = {The composition of the gut microbiota has been linked to acute stressors, suggesting that modulation of the gut microbiome is a potential avenue for enhancing human health and performance. The gut microbiome exerts its effects through several metabolites, which induce epigenetic and metabolic changes. Stress is a common occurrence in humans facing challenging environments such as military personnel and astronauts, but is not limited to humans. Among various species, crocodiles are well known for their "hardiness" and ability to achieve longevity, while surviving under stressful conditions. We speculated that their microbial gut flora produces substances contributing to their ability to resist stress, "wellbeing" and "longevity". Herein, we deliberate upon the stressors faced by individuals in testing conditions, and discuss potential avenues that can mitigate the gut microbiome compositional changes in order to augment human performance and overall health.},
}

@article {pmid41215576,
year = {2025},
author = {Hardegen, J and Amend, G and Wichard, T},
title = {The Microbiome of the Seaweed Cultivar Ulva compressa (Chlorophyta) and Its Persistence Under Micropollutant Exposure.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70230},
doi = {10.1111/1758-2229.70230},
pmid = {41215576},
issn = {1758-2229},
support = {//Graduietenakademie des Freistaats Thüringen/ ; 239748522//Deutsche Forschungsgemeinschaft/ ; 03ZU1214BB//Bundesministerium für Bildung und Forschung/ ; //European Cooperation in Science and Technology/ ; },
abstract = {The green macroalga Ulva demonstrates exceptional growth rates, robustness, adaptability and potential for nitrogen and phosphorus removal; thus, it is a promising candidate for wastewater treatment and bioremediation. However, micropollutants in wastewater pose a potential threat to the holobiont. We explored the effects of emerging contaminants found in groundwater and wastewater on the microbiome of the cultivar Ulva compressa (conspecific with Ulva mutabilis). We identified the core microbiome by comparing the microbiome of the long-term cultivar (cultivated under laboratory conditions for over 70 years) with the native microbiome of U. compressa. Long-term cultivation was found to homogenise and reduce microbiome diversity; however, key functional taxa, including algal growth and morphogenesis-promoting bacteria, persisted. We subsequently challenged the core microbiome of the U. compressa cultivar with four antibiotics (chloramphenicol, erythromycin, oxytetracycline and sulfamethoxazole), two herbicides (atrazine, glyphosate) and three endocrine disruptors (bisphenol A, estradiol and ethinylestradiol). The micropollutants exerted distinct impacts, with antibiotics showing stronger effects than hormonal disruptors, which Ulva rapidly removes from the culture medium. In contrast, the microbiome did not contribute to the removal of these substances. These results indicate that although Ulva's microbiome is sensitive to environmental change, key functions with positive implications for aquaculture and ecosystem management are retained.},
}

@article {pmid41215556,
year = {2025},
author = {Chen, W and Zhu, J and Chen, K and Zhou, A and Li, J and Ning, X and Kong, D},
title = {Oral Bacterial Predator with "Catch-and-Kill" Functionality for Bacterial Enteritis via Selective Pathogen Capture and Sonodynamic Elimination.},
journal = {ACS nano},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsnano.5c15064},
pmid = {41215556},
issn = {1936-086X},
abstract = {Bacterial enteritis necessitates innovative therapeutic strategies to overcome the significant limitations posed by conventional antibiotics. Here, we introduce a pioneering antibacterial approach, employing a multifaceted "catch-and-kill" mechanism that synergistically integrates targeted pathogen capture, sonodynamic eradication, and toxin neutralization. We present SonoMMT, a microfluidically engineered sonosensitizer-montmorillonite complex. SonoMMT selectively adsorbs pathogenic bacteria and bacterial toxins, shields encapsulated sonosensitizers from gastric degradation, and enables sonodynamic therapy. Upon ultrasound activation, SonoMMT generates localized reactive oxygen species (ROS), efficiently eliminating captured pathogens and neutralizing residual toxins while preserving host cell integrity. In vitro assessments demonstrate robust antibacterial efficacy against bacteria. In vivo studies using a Salmonella typhimurium (S. typhimurium)-induced enteritis mouse model confirm that orally delivered SonoMMT significantly reduces bacterial loads, toxin levels, intestinal inflammation, and tissue damage. Moreover, gut microbiome analysis reveals beneficial shifts in microbial composition post-treatment, underscoring SonoMMT's dual action in pathogen clearance and microbiome restoration. Thus, SonoMMT represents a transformative advancement in bacterial enteritis management.},
}

@article {pmid41214943,
year = {2025},
author = {Kim, YT and Kwak, JE and Kwon, JG and Lee, DY and Kim, HB and Lee, JH},
title = {Dietary intervention with sourdough and high-fiber breads enhances metabolic and microbial homeostasis in mice.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 3},
pages = {117433},
doi = {10.1016/j.foodres.2025.117433},
pmid = {41214943},
issn = {1873-7145},
abstract = {Sourdough (WBS) and high-fiber (HFB) breads are increasingly recognized for their metabolic health benefits. In this study, sourdough bread was prepared using lactic acid bacteria mixture (SPC Health Guard™), while Roman Meal whole grain bread served as the high-fiber bread variant. A 10-week mouse feeding experiment compared their physiological, immunological, and gut microbiome effects against conventional white bread (WB). Both WBS and HFB significantly reduced postprandial blood glucose levels and serum low-density lipoprotein (LDL) cholesterol. The incremental area under the curve (iAUC) of serum glucose was reduced by 61.7 % in WBS and 42.0 % in HFB groups. Notably, magnesium absorption was enhanced in the HFB group. Colonic cytokine analysis revealed decreased expression of pro-inflammatory markers (tumor necrosis factor-α; TNF-α, interleukin-6; IL-6) and increased anti-inflammatory interleukin-10 (IL-10) in both WBS and HFB groups, suggesting immune modulation through sourdough fermentation processes. Microbiome profiling showed HFB induced more extensive changes than WBS, enriching beneficial taxa including Eubacterium coprostanoligenes, Faecalibaculum, and Parasutterella, which are linked to lipid metabolism and anti-inflammatory effects. Metabolomic analysis identified shared elevations of DL-arginine and rhamnetin in both WBS and HFB groups, while HFB uniquely modulated amino acid and unsaturated fatty acid metabolism. Additionally, HFB-fed mice exhibited significantly higher levels of short-chain fatty acids (SCFAs), particularly acetate and propionate, reflecting enhanced microbial activity. Overall, both sourdough and high-fiber breads demonstrated metabolic and anti-inflammatory benefits. However, high-fiber bread showed broader effects on gut microbiota and metabolome remodeling, emphasizing the importance of dietary fiber in promoting host-microbe interactions and metabolic health.},
}

@article {pmid41214843,
year = {2025},
author = {Li, R and Li, F and Guo, H and Li, S and Wang, J and Wang, C},
title = {Coprophagy prevention interfered with intestinal barrier, lipid metabolism, and immune performance in rabbits via microbe-gut-liver axis.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {117},
pmid = {41214843},
issn = {2524-4671},
support = {SDAIT-21-10//Funds of Shandong Province Modern Agricultural Technology System Innovation Team Program/ ; ZR2023MC144//Natural Science Foundation of Shandong Province/ ; 3237306//National Natural Science Foundation of China/ ; },
}

@article {pmid41214813,
year = {2025},
author = {Corriero, A and Soloperto, R and Giglio, M and Salvagno, M and Trerotoli, P and Grasso, S and Ribezzi, M and Mosca, A and Petrillo, C and De Toma, N and Magnesa, G and Giacomucci, A and Accattoli, R and Gadaleta, RM and Florio, M and Cariello, M and Moschetta, A and Puntillo, F and Taccone, FS and Ranieri, VM},
title = {Probiotics to reduce ventilator-associated pneumonia in adults with acute non‑anoxic brain injury: Study Protocol for a Double-Blind Multicenter Randomized International Clinical Trial (PROACT).},
journal = {Trials},
volume = {26},
number = {1},
pages = {484},
pmid = {41214813},
issn = {1745-6215},
abstract = {BACKGROUND: Ventilator-associated pneumonia (VAP) remains a significant complication among critically ill patients, with associated mortality approaching 50%. Despite the implementation of established preventive strategies, additional interventions are urgently needed to further reduce the incidence of VAP. Probiotic therapy has emerged as a promising adjunctive approach; the benefits of probiotic therapy may be more pronounced in critically ill patients without pre-existing infections. The PROACT study will evaluate the prophylactic role of probiotics in a critically ill population with acute brain injury to reduce the VAP incidence, while also exploring microbiological endpoints and mortality to refine patient selection criteria.

METHODS: The PROACT study is a prospective, randomized, double-blind, placebo-controlled, multicenter trial designed to evaluate the efficacy of probiotic prophylaxis in adult critically ill patients requiring invasive mechanical ventilation following acute brain injury (e.g., head trauma, ischemic or hemorrhagic stroke). Patients with suspected pulmonary aspiration or pre-existing pulmonary infections at enrollment are excluded to reduce confounding. Participants are randomized in a 1:1 ratio to receive either a placebo (glucose polymer) or a probiotic formulation containing Lactobacillus acidophilus LA-5, Lactobacillus plantarum, Bifidobacterium lactis BB12, and Saccharomyces boulardii. The assigned intervention is administered twice daily via nasogastric tube and oropharyngeal application for up to 30 days or until intensive care unit (ICU) discharge. The primary endpoint is the incidence of VAP, as defined by current international guidelines, in the intention-to-treat (ITT) population. Secondary endpoints include the incidence of VAP in the modified intention-to-treat (mITT) population, catheter-related bloodstream infections, occurrence of sepsis and septic shock, 30-day all-cause mortality, ICU length of stay, and duration of mechanical ventilation. The study is powered at 80% (α = 0.05) to detect a clinically meaningful difference based on effect size estimates based on the PROVAP study, requiring a total sample size of 208 patients. All participating centers implement standard VAP prevention bundles as part of routine care.

DISCUSSION: By evaluating the efficacy of probiotic therapy in preventing VAP and the impact on mortality among critically ill brain-injured patients, this trial has the potential to generate high-quality evidence supporting the incorporation of probiotics into standard VAP prevention protocols. The findings may have significant implications for clinical practice guidelines and public health policy related to infection control and microbiome-targeted interventions in the intensive care setting.

TRIAL REGISTRATION: Registered at ClinicalTrials.gov (identifier: [NCT06092554]). Registered on 2023-10-15.},
}

@article {pmid41214749,
year = {2025},
author = {Huang, Y and Dai, S and Ma, W and Sun, Y and Xu, Y and Wang, H and Meng, L and Huang, Y and He, C and Shen, R and Luo, Y and Teng, Y},
title = {Decoding the microbial assembly and environmental drivers along the phyllosphere-rhizosphere continuum of leguminous green manure Astragalus sinicus.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {140},
pmid = {41214749},
issn = {2524-6372},
support = {42130718//National Natural Science Foundation of China/ ; SQ2022RA24910167//National Science and Technology Innovation Leading Talents Program/ ; },
abstract = {Green manure crops are increasingly recognized not only for their contributions to soil fertility but also for their role in shaping plant-associated microbiome. Astragalus sinicus, a widely used leguminous green manure in East Asian paddy fields, harbors distinct microbial assemblages across plant compartments, yet the ecological processes driving microbiome assembly along its phyllosphere-rhizosphere continuum remain unclear. In this study, we profiled microbiome composition across the rhizospheric, phyllospheric, and soil compartments of A. sinicus using 16S rRNA gene amplicon sequencing targeting the region south of the Yangtze River, analyzing 315 samples collected from seven rice-growing regions. We found that Proteobacteria predominated all sampled compartments, with Mesorhizobium (75.85-96.93%) constituting the predominant taxon in the root microbiome. The leaf microbiome showed higher variability, dominated by Vibrionimonas (0.31-46.6%), Pantoea (0.71-46.61%), Pseudomonas (0.07-24.6%) and Bradyrhizobium (0.06-8.45%). Co-occurrence networks revealed a distinct gradient, including expansive yet weakly connected soil networks, moderately sized and highly modular leaf networks, and compact, highly robust root consortia, delineating a shift from environmentally driven complexity to host-filtered stability. Root and leaf microbiome assembly was primarily governed by stochastic processes (- 2 < β-NTI < 2, NCM r[2] > 70%) and plant- mediated selection (DI = 0.01/0.02, DSI = 0.09/0.14), with soil nutrient conditions, particularly total nitrogen, organic carbon, available phosphorus, and available potassiu, playing significant roles in shaping microbiome composition (p < 0.05). These core plant-associated ASVs were selectively enriched by the plant from the soil in over 70% of the sampled regions. Among these, Mesorhizobium in roots and Methylobacterium-Methylorubrum in leaves were found to be critical for nitrogen fixation and nutrient cycling, as evidenced by previous studies. Our results highlight the intricate interactions between plants, microbes, and their environment, underscoring the importance of plant-mediated selection and soil nutrient conditions in shaping the microbiome of A. sinicus, with significant implications for sustainable agricultural practices.},
}

@article {pmid41214535,
year = {2025},
author = {Wang, R and Wang, M and Wang, J and Wang, P and Ou, J and Tang, W and Sun, G and Wang, Q and Cheng, X and Huang, Y and Chen, J and Zhang, Z and Ren, C},
title = {Transport stress alters serum biochemistry and gut microbiota in Tibetan sheep (ovis aries): a 30-day recovery assessment.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {726},
pmid = {41214535},
issn = {1471-2180},
support = {2022-NK-134//The Science and Technology Program of Qinghai Province/ ; 2023AH050981//The Scientific Research Project of Anhui Higher Education Institutions/ ; CARS-38//The National Modern Meat Sheep Industry Technology System/ ; },
abstract = {BACKGROUND: Transport stress poses a major challenge to the livestock industry. Studies have shown that transportation stress can cause depression, elevated body temperature and dysbiosis of intestinal microbiota in meat goats, and in severe cases, even lead to death of the animals, which in turn affects the economic efficiency of the farming industry. However, the changes in blood biochemical indicators and flora of Tibetan sheep throughout the receiving period after long-distance transport remain unclear.

METHODS: In this study, six 7-month-old Tibetan sheep with similar body weights were selected for a 30-d transport trial, and blood and faecal samples were collected for blood biochemical indices and 16 S microbiome sequencing before transport (BT), and on day 1 (AT 1), day 16 (AT 16), and day 30 (AT 30) after the end of the transport, respectively.

RESULT: And a number of blood biochemical indices (creatine kinase (CK), lactate dehydrogenase (LDH), alkaline phosphatase (ALP), aspartate aminotransferase (AST), cortisol (COR), and adrenocorticotropic hormone (ACTH)) were significantly elevated (P < 0.05). Combined analysis of physiological and biochemical indices with 16 S rDNA sequencing showed that Turicibacter, Romboutsia and Clostridium_sensu_stricto_1 were positively correlated with LDH, ALP, CK, AST, and ACTH, while Prevotellaceae_UCG_004 was negatively correlated. Furthermore, the observed recovery trends in vital signs after AT 16 suggest that Tibetan sheep may be able to adapt to the new environment within one month post-transport. The present study illustrated the effects of transport without measures on the vital signs, serum biochemical indicators and faecal microorganisms of Tibetan sheep throughout the receiving period, which is of great significance in guiding the transport of Tibetan sheep and solving the damage caused by transport stress on the economic benefits of the farming industry.},
}

@article {pmid41214530,
year = {2025},
author = {Chen, JS and Tu, MJ and Chang, YM and Tu, YF and Chiang, CW},
title = {Probiotics restore GABAergic neurons and attenuate postnatal seizures in periventricular leukomalacia.},
journal = {Nutritional neuroscience},
volume = {},
number = {},
pages = {1-14},
doi = {10.1080/1028415X.2025.2574964},
pmid = {41214530},
issn = {1476-8305},
abstract = {Objectives: Postnatal epilepsy often arises after periventricular leukomalacia (PVL) in preterm infants and resists to treatment. Its underlying mechanisms and potential preventive strategies remain unclear. Probiotics, known to alleviate microbial dysbiosis and reduce inflammation, may offer therapeutic benefits.Methods: PVL injure was conducted using a combination of hypoxia-ischemia and lipopolysaccharide treatment. The rats were evaluated for seizure susceptibility, neuroinflammation, GABAergic neurons, and gut microbiota composition before and after probiotic administration. The probiotic formulation included Lactobacillus rhamnosus, Lactobacillus casei, Bifidobacterium bifidum, Bifidobacterium lactis, Bifidobacterium longum and Bifidobacterium breve in galacto-oligosaccharide and Fructooligosaccharides.Results: PVL rats exhibited microgliosis, reduced density of premyelinating oligodendrocytes, and decreased myelin expression (all P < 0.05). At postnatal days 85-90, these rats showed a significantly higher frequency of electrographic seizures and longer total seizure duration (P < 0.05). A significant reduction in cortical GABAergic neurons, particularly somatostatin-positive interneurons, was also observed in PVL rats compared to controls (P < 0.01). Treatment with probiotics restored GABAergic neurons and significantly reduced seizure frequency and duration (P < 0.05). Additionally, probiotics modulated gut microbiota composition and increased levels of butyric acid in both fecal samples and cerebrospinal fluid (CSF) (P < 0.05). Probiotic treatment also reduced cortical microglial activation and lowered CSF levels of the proinflammatory cytokine TNF-α.Conclusion: Probiotic supplementation may reduce seizure activity following PVL brain injury by mitigating neuroinflammation and restoring GABAergic neurons via the gut-brain axis. These findings suggest that probiotics could serve as a promising adjuvant therapy for preventing epilepsy after PVL.},
}

@article {pmid41214302,
year = {2025},
author = {Wang, W and He, W and Zhang, Y and Wang, X and Li, J and Zhang, X and Chu, B and Nie, Y and Portal-Gonzalez, N and Santos-Bermudez, R},
title = {Metabolome-driven microbiome assembly in ginger (Zingiber officinale) enhances nutrient cycling and crop yield through keystone taxa.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1547},
pmid = {41214302},
issn = {2399-3642},
support = {32201546//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Plant microbiomes shape crop performance, but the mechanisms by which host-derived metabolites influence the recruitment and organisation of beneficial microbes-and how these affect crop yield-remain poorly understood. Few studies have linked multi-kingdom microbiome structure, metabolite profiles, and agronomic traits under field conditions. We integrated 16S rRNA and ITS amplicon sequencing with untargeted LC-MS/MS metabolomics across 36 samples from two Zingiber officinale (ginger) cultivars with contrasting yields. Bacterial communities were primarily shaped by stochastic processes (neutral model R[2] = 0.67-0.68), while fungal assembly was deterministic (βNTI < -2 in roots and rhizomes). The high-yield cultivar exhibited more complex co-occurrence networks (596 vs. 272 edges) and enrichment of keystone taxa, including Talaromyces and Devosia. Metabolomic profiling identified 586 unique compounds, with 24 enriched pathways in the high-yield cultivar, notably isoflavonoid biosynthesis and folate metabolism. Key host metabolites-Niazimin A and 1-oleoyl-lysophosphatidic acid-showed strong positive correlations (r > 0.75, P < 0.01) with nitrogen-fixing and growth-promoting microbes, whereas Oxindole correlated negatively. These findings suggest that host metabolic shifts and keystone microbes co-regulate microbiome structure and nutrient cycling. Our results provide mechanistic insight into microbiome-mediated yield differences and a basis for microbiome-informed crop design.},
}

@article {pmid41213205,
year = {2025},
author = {De Alcaraz-Fossoul, J and Wang, Y and Marshall, PA and Liu, R and Broatch, J and Stasulli, NM and Cook, GD},
title = {A first examination of skin-transferred microbiota demonstrates the feasibility of utilizing microbes to determine the age of latent fingerprints: A proof-of-concept study.},
journal = {Forensic science international},
volume = {378},
number = {},
pages = {112710},
doi = {10.1016/j.forsciint.2025.112710},
pmid = {41213205},
issn = {1872-6283},
abstract = {Friction ridge skin patterns, including latent fingerprints (LFs), have long been essential for human identification. However, traditional ridge examinations do not convey temporal information. The ability to estimate the Time-since-Deposition (TsDp) of LFs could provide valuable chronological context in criminal investigations, helping to reconstruct timelines and corroborate alibis. A recent study explored LF microbiota as potential biological "clocks" for TsDp estimations at the Phylum taxonomical rank. In that instance, it was revealed that the composition, relative abundance, and succession patterns of microorganisms varied over time. This dynamic nature made the transferred skin microbiome a promising candidate for investigating predictable temporal changes of LFs in semi-controlled environments, such as indoor locations. The present article further expands the taxonomic resolution of the original study by identifying time-dependent microbial taxa at the Family rank and suggesting specific temporal signatures through statistical analyses. The same experimental conditions were considered: three donors, hand washing conditions, and aging for 1, 7, 14, and 21 days. For this analysis, the relative abundance, presence, and temporal shifts were examined with a focus on time-variant taxa. The 16S rRNA gene (V4 region) sequencing revealed distinct temporal signatures across the observed time points and handwashing conditions. For example, in unwashed hands, the combined presence of Mycosphaerellaceae and Coxiellaceae indicated a freshly deposited LF. In contrast, under washed conditions, the presence of Ruminococcaceae and Beijerinckiaceae was associated with a recent deposition. These preliminary findings further demonstrate the potential of microbiome analysis as a forensic tool for estimating TsDp in LFs and are a feasibility study for further work.},
}

@article {pmid41213144,
year = {2025},
author = {Straka, M and Borecová, P and Straka, M},
title = {Periodontitis, Fusobacterium nucleatum, and Colorectal Carcinoma. A Review.},
journal = {Neuro endocrinology letters},
volume = {46},
number = {4},
pages = {},
pmid = {41213144},
issn = {2354-4716},
abstract = {Our review study addresses chronic periodontitis and its potential complications in the distal segments of the intestine and rectum. Subgingival colonization by gram-negative anaerobic bacteria such as Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Eikenella corrodens, and Fusobacterium nucleatum may, through haematogenous dissemination into non-oral tissues and organs, cause severe systemic diseases. In connection with colorectal carcinoma, the third most frequently diagnosed malignant tumor, special attention has been focused on the anaerobic rod Fusobacterium nucleatum, one of the key periodontal pathogens involved in periodontal pocket infections. A growing amount of direct and indirect evidence supports its role in the development, progression, and persistence of colorectal carcinoma in the distal colon and rectum. F. nucleatum possesses numerous virulence factors that underlie its remarkable infectious potential, not only within the oral cavity but also in the colonic environment, where they facilitate its integration into the dysbiotic microbiome and directly contribute to carcinogenesis in this region. Disruption of the physiological microbiota and colonization by F. nucleatum are now considered major drivers of malignant tumorigenesis in the distal colon. Several studies confirm the oral origin of F. nucleatum and its potential haematogenous spread into the intestinal microenvironment. Eradication of F. nucleatum from the colon is regarded as a crucial factor in achieving successful treatment outcomes for colorectal cancer (CRC). However, systemic administration of broad spectrum antibiotics adversely affects the composition of the normal gut microbiome, leading to microbial imbalance. For this reason, the elimination of F. nucleatum in the colon and rectum relies on a whole range of antibacterial agents that minimally disrupt the gut microbiota. Our eradication strategy for F. nucleatum emphasizes close cooperation between dentists or periodontologists and gastroenterologists or oncologists, targeting high-risk populations: patients with IBD, colorectal adenomas ≥1 cm, multiple polyps, or first-degree relatives with CRC diagnosed before age 60. These at risk patients undergo dental evaluation for periodontitis and gingivitis by collaborating dentists. Identified cases are treated using localized, comprehensive, and early eradication strategies targeting F. nucleatum and other periodontal pathogens within the periodontal pocket microenvironment. The primary objective of early interdisciplinary cooperation is to detect early stages of periodontitis with periodontal pocket depths of up to 4 mm. In such early forms of periodontitis, elimination of infection can be achieved through local approaches including scaling, deep scaling, and curettage, combined with the application of antibacterial solutions, varnishes, antimicrobial impregnated fibers, and, where appropriate, the use of periodontal lasers.},
}

@article {pmid41213120,
year = {2025},
author = {Wei, HJ and Lei, JJ and Wei, XL and Gou, W and Han, JH and Yu, C},
title = {Bacillus proteolyticus Enhances the Biocontrol of Needle Cast in Cathaya argyrophylla by Modulating Physiological Pathways and the Phyllosphere Microbiome.},
journal = {Phytopathology},
volume = {},
number = {},
pages = {},
doi = {10.1094/PHYTO-11-24-0346-R},
pmid = {41213120},
issn = {0031-949X},
abstract = {Cathaya argyrophylla, a relict species endemic to China in the Pinaceae family, is classified as endangered on the IUCN Red List of Threatened Species. Needle cast caused by the fungal pathogen Neofusicoccum parvum is one of the most prevalent diseases affecting C. argyrophylla, leading to needle discoloration and necrosis, which poses a serious threat to its growth. Currently, there is a lack of effective biological control methods for this disease. In this study, we isolated an endophytic bacterium, Bacillus proteolyticus X6-1, from healthy needles of C. argyrophylla. This strain demonstrated a 65.5% inhibition of N. parvum in vitro. The pot experiment demonstrated that after inoculation with B. proteolyticus X6-1, the disease incidence and index of needle cast in C. argyrophylla were reduced by 42% and 20.3% respectively. Given its potential efficacy against needle cast in C. argyrophylla, we employed co-culture techniques alongside transcriptomics and high-throughput sequencing to elucidate the biological control mechanisms of strain X6-1. Furthermore, X6-1 enhanced the photosynthetic activity and antioxidant enzyme levels of C. argyrophylla. Inoculation with the B. proteolyticus strain further altered the phyllosphere microbiome by promoting the enrichment of beneficial microorganisms while decreasing the abundance of Neofusicoccum spp. Transcriptomic analysis revealed that B. proteolyticus regulates key biological pathways associated with growth in C. argyrophylla. Moreover, strain X6-1 produces protease and β-glucanase enzymes, which which may contribute to its antifungal activity. Collectively, these findings suggest that B. proteolyticus may serve as an effective biocontrol agent for managing needle cast in C. argyrophylla.},
}

@article {pmid41213078,
year = {2025},
author = {Elasbali, AM and Adnan, M and Ali, AS and Shamsi, A and Hassan, MI},
title = {Multi-Omics Advances in Major Depressive Disorder for Molecular Insights, Biomarker Discovery, and Therapeutic Development.},
journal = {Aging and disease},
volume = {},
number = {},
pages = {},
doi = {10.14336/AD.2025.1075},
pmid = {41213078},
issn = {2152-5250},
abstract = {Major depressive disorder (MDD) affects hundreds of millions worldwide and remains a major unmet clinical need because conventional monoaminergic agents achieve remission in fewer than half of patients and leave a substantial treatment-resistant subgroup. To address this gap, integrative multi-omics approaches, combined with computational systems biology, are being used to dissect its multifactorial etiology. Here, we review key findings from large Genome-wide association studies (GWAS), single-cell and spatial transcriptomics, proteomics, and metabolomics that converge on disrupted neuroplasticity, immune-inflammatory signaling, HPA-axis dysregulation, mitochondrial metabolism, and gut-brain interactions. We describe how AI-driven network modeling and structure-based drug design (SBDD) are translating multi-omics signals into candidate biomarkers and mechanism-based therapeutics, for example, N-methyl-D-aspartate/glutamatergic modulators, kappa opioid antagonists, anti-inflammatory agents, and epigenetic modulators. We highlighted the clinical implications, specifically molecularly stratified biomarkers for patient selection, trial enrichment, and structure-guided optimization of rapid-acting antidepressants and microbiome-based interventions. Finally, we discuss the limitations and immediate translational priorities that emphasize the trajectory from multi-omics discovery to precision psychiatry for MDD.},
}

@article {pmid41212895,
year = {2025},
author = {Shao, H and Yuan, C and Qiang, J and Hua, W and Cheng, Y and Wang, W},
title = {Thermophilic microbiome acclimation for enhanced anaerobic digestion of food waste: Optimization and performance evaluation.},
journal = {PloS one},
volume = {20},
number = {11},
pages = {e0336355},
pmid = {41212895},
issn = {1932-6203},
abstract = {Thermophilic anaerobic digestion (TAD) represents a promising approach for food waste (FW) treatment, offering significant advantages including accelerated reaction rates and increased volumetric biogas yield. However, the practical application of TAD is hindered by both the limited availability of thermophilic methanogenic consortia and heightened sensitivity to organic loading rate (OLR) fluctuations. In this study, a two-stage temperature shift strategy from mesophilic to thermophilic was implemented to establish a stable methanogenic community. The results showed that daily biogas yield increased steadily with rising fermentation temperature, reaching to a peak of 671.2 ml at 55 °C, which were 60.8% higher than that of mesophilic digestion. Microbial community analysis revealed that TAD increased the abundance of dominant hydrolytic bacteria (e.g., Defluviitoga) and hydrogenotrophic methanogen (e.g., Methanoculleus), consequently enhancing biogas production efficiency. Moreover, gradually increasing the OLR from 1.5 to 4 g VS/(L·d) significantly enhanced both biogas production and CH4 content, achieving a peak daily biogas yield of 2264.8 ml with sustained CH4 concentration stability (72-76%).},
}

@article {pmid41212647,
year = {2025},
author = {Hamdi, A and Stathopoulou, P and Gharbi, A and Saadouli, I and Najjari, A and Kacem, I and Ouzari, HI and Bel Mokhtar, N and Tsiamis, G and Gouider, R and Klibi, N},
title = {Salivary microbiome dysbiosis in patients with Alzheimer's disease.},
journal = {Journal of Alzheimer's disease : JAD},
volume = {},
number = {},
pages = {13872877251393229},
doi = {10.1177/13872877251393229},
pmid = {41212647},
issn = {1875-8908},
abstract = {BackgroundInvestigating human oral microbiota is now of great interest, being clinically significant for general and oral health. Many research studies have started to focus on the link between oral microbial dysbiosis and Alzheimer's disease. However, little is known about North African populations.ObjectiveWe aimed to distinguish the dissimilarity in the structure of microbial oral flora between the Alzheimer's disease patients and healthy controls in a Tunisian population.MethodsWe investigated the salivary microbiota using next-generation shotgun sequencing.ResultsThe overall structure of the oral microbial community of the Alzheimer's disease patient group was obviously different from the healthy control group. Significantly higher levels of Haemophilus (25.26%) were noticed in the AD group. However, Neisseria (10.17%) showed lower levels compared to the HC group. Considering the disease severity, Selenomonas and Aggregatibacter showed gradually higher levels as the disease progressed. Porphyromonas showed the highest levels in the mild stage of the disease, while Treponema, Selenomonas, and Peptostreptococcus were associated with severe stage. The presence of key taxa, Aggregatibacter and Selenomonas may constitute a dysbiosis signature in individuals with AD.ConclusionsThese findings may be of high relevance for orienting further studies on evaluating the physio-pathological process, confirming the implication of oral microbiota in AD and opening diagnostic and therapeutic avenues.},
}

@article {pmid41212512,
year = {2025},
author = {Eraghieh Farahani, H and Pourhajibagher, M and Asgharzadeh, S and Bahador, A},
title = {Postbiotics: Novel Modulators of Gut Health, Metabolism, and Their Mechanisms of Action.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41212512},
issn = {1867-1314},
abstract = {Postbiotics, defined as non-viable microbial cells, structural components, or metabolites, have recently emerged as promising modulators of gut health and metabolism. Unlike probiotics, they circumvent safety concerns associated with live microorganisms, including potential translocation, antibiotic resistance transfer, and viability loss during storage. Postbiotics encompass diverse bioactive compounds such as short-chain fatty acids (SCFAs), exopolysaccharides, bacteriocins, antioxidant enzymes, surface layer proteins, and bacterial lysates, each exerting distinct biological effects. Mechanistically, they enhance epithelial barrier function, regulate innate and adaptive immune responses, and modulate host gene expression through pattern recognition receptors and epigenetic modifications. SCFAs, particularly butyrate and propionate, improve intestinal homeostasis, insulin sensitivity, and anti-inflammatory signaling, while bacteriocins and EPSs display antibacterial, antiviral, anticancer, and immunomodulatory properties. Postbiotics also interfere with viral replication, inhibit pathogen adhesion, and attenuate inflammatory pathways, highlighting their multifunctional roles. Compared to probiotics and prebiotics, they offer superior safety, chemical stability, and clinical applicability, especially in vulnerable populations such as infants, elderly individuals, and immunocompromised patients. Preclinical and in vitro studies provide compelling evidence for their therapeutic potential in metabolic disorders, infections, cancer, and immune-mediated diseases; however, clinical data remain limited. Further research is required to establish standardized definitions, optimal formulations, dosing strategies, and regulatory frameworks to support their integration into functional nutrition and precision medicine. Collectively, postbiotics represent a next-generation approach to microbiota-targeted interventions, offering novel opportunities for disease prevention, adjunctive therapy, and the advancement of microbiome-based therapeutics.},
}

@article {pmid41212444,
year = {2025},
author = {Caslin, HL and Williams, JW},
title = {Mechanisms of Innate Immune Modulation by High-Fat Diet: Implications for Obesity and Asthma.},
journal = {Current allergy and asthma reports},
volume = {25},
number = {1},
pages = {51},
pmid = {41212444},
issn = {1534-6315},
support = {25TPA1471583//American Heart Association/ ; 25TPA1471583//American Heart Association/ ; },
abstract = {PURPOSE OF THE REVIEW: The innate immune system plays a critical role in mediating many of the physiological consequences of high-fat diet consumption. Dietary lipids, and specifically saturated fatty acids like palmitate and stearate, directly activate innate immune cells and alter the composition of the gut microbiome. Moreover, long-term high-fat diet feeding can induce chronic inflammation, adipose expansion, and the development of obesity. High-fat diet consumption and obesity also worsen the risk for chronic diseases like asthma.

RECENT FINDINGS: It is well known that high-fat diet feeding activates innate immune cells and alters the gut microbiome. However, emerging research provides new insight into the mechanisms by which high-fat diet feeding and obesity affect innate immunity and further disease development. These emerging mechanisms include the induction of lipid-associated macrophages (LAMs), innate immune memory, and innate-adaptive crosstalk leading to T cell exhaustion and granzyme K production. These novel mechanisms help us better understand the effect of high-fat diets on innate immunity, and future studies in these areas may help us better identify new therapeutic strategies for managing obesity and asthma.},
}

@article {pmid41212427,
year = {2025},
author = {Vallianou, NG and Kounatidis, DC and Geladari, EV and Evangelopoulos, A and Kaldis, V and Stratigou, T and Evangelopoulos, AA and Karampela, I and Dalamaga, M},
title = {Climate Change, Air Pollution and the Global Obesity Syndemic: a Review of Current Evidence.},
journal = {Current obesity reports},
volume = {14},
number = {1},
pages = {78},
pmid = {41212427},
issn = {2162-4968},
abstract = {PURPOSE OF REVIEW: Climate change and obesity are two converging global crises with complex and interrelated pathways. This review aims to synthesize recent evidence linking climate-related exposures, including rising ambient temperatures, air pollution, and urbanization to the pathogenesis of obesity. It also explores how obesity itself increases vulnerability to heat injury and environmental stress, highlighting the bidirectional nature of this syndemic.

RECENT FINDINGS: Epidemiologic evidence has supported associations between air pollution and increased body mass index, central adiposity, and metabolic dysfunction across the lifespan. Mechanistic research implicates impaired thermogenesis, chronic inflammation and oxidative stress, endocrine disruption, hypothalamic inflammation, and microbiome dysbiosis as key pathways linking environmental exposures to adiposity. Obesity further amplifies the physiological burden of climate-related stressors, such as heatwaves, due to reduced heat dissipation and altered hormonal responses. Anti-obesity medications may exacerbate heat-related risks via dehydration and gastrointestinal side effects. Urban greenness appears to offer a partial protective effect, modulating the obesogenic impact of air pollution and heat, particularly in low-income settings. Obesity and climate change share common socioeconomic, behavioral, and environmental drivers. Addressing this dual burden requires integrated strategies that promote environmental sustainability and metabolic health. These include green infrastructure, active transportation, climate-adapted clinical care, and public health strategies that reflect planetary health principles. Recognizing obesity not only as a medical condition but also as an environmentally influenced disorder is essential for effective, future-oriented prevention and intervention efforts.},
}

@article {pmid41212347,
year = {2025},
author = {Li, SW and Wang, HC and Chen, MS},
title = {Erianin is a therapeutic candidate for addressing neuroinflammation triggered by intracerebral hemorrhage.},
journal = {Langenbeck's archives of surgery},
volume = {411},
number = {1},
pages = {10},
pmid = {41212347},
issn = {1435-2451},
abstract = {BACKGROUND: Neuroinflammation is a common consequence of intracerebral hemorrhage (ICH), leading to neurological impairments. Research indicates that the gut microbiome can influence neuroinflammatory responses. Erianin, is a potential therapeutic agent in the treatment of inflammation. Yet, the specific impact of erianin on ICH-induced inflammation and its interaction with the gut microbiome remain areas of ongoing investigation.

METHODS: ICH mouse model was established and treated with erianin. Neurobehavioral tests, brain water content, immunofluorescence, western blotting, and terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) staining were performed to measure the neurological defects and neuroinflammation and neuron apoptosis. Immunofluorescent staining and western blotting assay were performed to assess the activation states of microglia and inflammation. The quantitative real-time polymerase chain reaction (qRT-PCR), enzyme-linked immunosorbent assay (ELISA), and FITC-dextran assays were utilized to measure the intestinal barrier integrity. The composition of the gut microbiota was analyzed by sequencing the 16 S rRNA extracted from fecal samples.

RESULTS: Administration of Erianin notably decreased inflammation in the brain and improved neurological function in ICH mice by inhibiting the proinflammatory activation of microglia. Additionally, Erianin bolstered intestinal barrier integrity, evidenced by decreased levels of lipopolysaccharide-binding protein. Furthermore, treatment with Erianin led to observable shifts in the gut microbiota. Notably, the activation of the ERK signaling pathway was found to counteract the neuroprotective effects of Erianin following ICH.

CONCLUSIONS: Erianin is a therapeutic candidate for addressing neuroinflammation triggered by ICH, with its mechanisms of action likely involving the modulation of ERK signaling and the gut microbiome.},
}

@article {pmid41212059,
year = {2025},
author = {Vladar, EK and Gillen, AE and Yadav, S and Murphree, MR and Baraghoshi, D and Harris, JK and Pruesse, E and Niemiec, SS and Wilson, AW and Hisert, KB and Humphries, SM and Strand, M and Lynch, DA and Seibold, MA and Beswick, DM and Taylor-Cousar, JL},
title = {Transcriptomic and functional responses of the cystic fibrosis airway epithelium to CFTR modulator therapy.},
journal = {JCI insight},
volume = {10},
number = {21},
pages = {},
doi = {10.1172/jci.insight.196018},
pmid = {41212059},
issn = {2379-3708},
abstract = {Elexacaftor/tezacaftor/ivacaftor (ETI) cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapy has led to rapid and substantial improvements in cystic fibrosis (CF) airway disease. Underlying molecular and cellular mechanisms, long-term efficacy, and ability to reverse airway epithelial remodeling in established disease remain unclear. Longitudinal nasal brushes from an adult CF cohort were used to evaluate gene expression, cellular composition, stem cell function, and microbiome changes at baseline and at 6 months and 2 years after ETI. The baseline to 6 month span showed a massive downregulation of extensive neutrophilic inflammatory gene expression programs that correlated with increased pulmonary function and decreased sinusitis. Primary airway epithelial stem cell cultures from matched donor samples showed partially improved differentiation and barrier capacity at 6 months. Although clinical outcomes remained stable during the 6 month to 2 year span, transcriptional changes revealed a resurgence of baseline inflammatory programs. The time course of gene expression was consistent with ongoing normalization of epithelial remodeling. Relative abundance of Pseudomonas also decreased during the time course. These data suggest that ETI rectifies inflammation, epithelial remodeling, and bacterial infection in the airways, but resurgence of inflammatory gene expression may indicate ongoing inflammation, potentially presaging disease progression with long-term therapy.},
}

@article {pmid41212006,
year = {2025},
author = {Alshevskaya, AA and Aksenova, EI and Khasanov, RY},
title = {[Thematic priorities in oncology: analytical overview of publication trends and vectors of translational growth].},
journal = {Problemy sotsial'noi gigieny, zdravookhraneniia i istorii meditsiny},
volume = {33},
number = {0},
pages = {1069-1074},
doi = {10.32687/0869-866X-2025-33-s2-1069-1074},
pmid = {41212006},
issn = {0869-866X},
abstract = {Amid the rapid expansion of biomedical publications and the increasing complexity of the oncology research landscape, there is a growing need for a systematic analysis of thematic priorities that define global and national trajectories of scientific advancement. Oncology, as a field at the forefront of interdisciplinary innovation, spans domains from immune and cellular technologies to molecular imaging and epigenetic targets. Identifying frontier research areas that combine high scientific intensity, sustained international relevance, and translational potential is becoming a key tool for science policy and strategic planning. This study aims to map the most prominent oncology-related topics that emerged between 2021 and 2025, using data from the SciVal platform. A content-bibliometric analysis was conducted on the twenty leading thematic clusters in global oncology, followed by a comparative assessment of their representation in the Russian publication landscape. Metrics analyzed included publication output, field-weighted citation impact (FWCI), engagement dynamics, and institutional distribution. The results indicate that Russian research is contributing to several key topics, exhibiting high citation performance in niche areas such as exosomes, CAR-T therapy, radiomics, and immunotherapy for non-small cell lung cancer. However, many globally significant topics remain underrepresented in the Russian agenda, reflecting structural and human resource gaps in areas such as epigenetics, microbiome studies, precision immunomodulation, and regulated cell death mechanisms. These findings highlight both thematic gaps and institutional growth zones that require targeted support. Identifying advanced research areas positioned at the interface of scientific innovation and clinical applicability may inform the modernization of research infrastructure, the prioritization of national grant programs, and the integration of Russian research centers into global scientific consortia.},
}

@article {pmid41211992,
year = {2025},
author = {Wang, Y and Tian, F and Zhang, J and Xu, S and Li, M and Tong, Y},
title = {Identification and characterization of a novel plaque-invisible lytic single-stranded RNA phage.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0163724},
doi = {10.1128/jvi.01637-24},
pmid = {41211992},
issn = {1098-5514},
abstract = {The RNA phages offer promising applications in biotechnology, including vaccine development and drug delivery. However, their potential remains underexplored due to the limited number of known RNA phages, partly because conventional methods fail to identify plaque-invisible lytic phages that do not form plaques. Here, we introduced a novel method that combines RNA-inclusive metagenomic studies and quantitative reverse transcription-PCR (RMS-RT-qPCR) to identify and characterize active RNA phages from environmental samples. This study led to the discovery of a new active Qbeta-like phage, named Cute. Genomic analysis revealed that Cute is a new member of the Qubevirus genus. Although Cute does not form plaques, it can be observed to continuously release into the supernatant when co-cultured with the host by RT-qPCR detection. This discovery underscores the potential diversity of RNA phages in nature and the limitations of traditional culture-dependent techniques. Our findings suggest that RMS-RT-qPCR could aid in the discovery of active RNA phages with significant biotechnological applications.IMPORTANCEThe discovery and characterization of RNA phages might be historically constrained by traditional culture-based methods. Our study provides a powerful tool for identifying active RNA phages by combining RNA-inclusive metagenomic analysis with RT-qPCR. This method expands our understanding of the diversity and ecological roles of RNA phages, which are often overlooked in microbiome studies. This research highlights the importance of RNA phages in natural ecosystems and their potential applications in biotechnology and medicine, such as antimicrobial therapies and vaccine development. By expanding our understanding of RNA phage diversity, this study opens new avenues for their utilization in various fields, emphasizing the need for continued exploration of these versatile biological entities.},
}

@article {pmid41211986,
year = {2025},
author = {Huang, Y and Wan, J and Shu, C and Yan, X and Ma, J and Zhang, T and He, J and Wan, Z and Li, G and Zhang, Q and Zhou, Z and Sun, X and Zhao, J and Zhang, P and Wang, L and Zhang, T and Tian, Q},
title = {Impact of oral Chlamydia vaccination on host gut microbiome and metabolite composition.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0128525},
doi = {10.1128/msystems.01285-25},
pmid = {41211986},
issn = {2379-5077},
abstract = {Chlamydia trachomatis, an intracellular pathogen, is recognized as the most common sexually transmitted bacterial infection among women worldwide. Chlamydia infections can lead to undesirable clinical outcomes, including pelvic inflammatory disease and infertility. Recently, the gut has been identified as a niche for Chlamydia colonization in human gut-derived organoids. However, despite the biological impact on the host remaining under investigation, oral inoculation of Chlamydia as a whole-organism vaccine has been reported as a promising strategy for preventing genital Chlamydia infections in mice. Few studies have evaluated the impact of oral Chlamydia vaccination on the gut microbiome and metabolite changes. In this study, we assessed time-series alterations in the gut microbiome and metabolites following oral Chlamydia muridarum inoculation in a mice model, and we analyzed the composition and correlation between serum immune parameters and the sequencing profiles in the host. We identified 129 microbial changes and 186 differentially abundant metabolites in the gut across various vaccination approaches during the 30-day immunization process. Additionally, we discussed the potential influence of live Chlamydia on gut epithelium and the biomarkers of effective immunization based on correlation analysis.IMPORTANCEChlamydia infections primarily lead to morbidity rather than mortality. Consequently, in developing and implementing a Chlamydia vaccine, the utmost priority is evaluation of safety. As a promising yet controversial approach, live oral vaccination for Chlamydia raises concerns regarding its impact on the host's gut environment. Our study not only investigates changes in the gut microbiome and metabolites during vaccination but also identifies changes in gut epithelium during vaccination and potential biomarkers during immunization. These findings are crucial for the development of whole-organism oral Chlamydia vaccines and provide valuable insights into the long-term colonization of Chlamydia in the gut.},
}

@article {pmid41211985,
year = {2025},
author = {Hypša, V and Martinů, J and Mahmood, S and Gupta, S and Nováková, E and Roth, S and Balvín, O},
title = {Dynamic but constrained: repeated acquisitions of nutritional symbionts in bed bugs (Heteroptera: Cimicidae) from a narrow taxonomic pool.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0124725},
doi = {10.1128/msystems.01247-25},
pmid = {41211985},
issn = {2379-5077},
abstract = {Bed bugs (Heteroptera: Cimicidae) harbor obligate bacterial symbionts that supplement their blood diet with missing nutrients, especially B vitamins. The primary symbiont, transovarially transmitted Wolbachia, is notable for a horizontally acquired biotin operon. Additional maternally inherited bacteria, including Symbiopectobacterium and Tisiphia, have been detected but are considered facultative and nonessential. However, nearly all current knowledge is derived from the human-associated Cimex lectularius, leaving symbiont diversity across more than 100 bed bug species largely unknown. Using amplicon and metagenomic data, we identified Wolbachia, Symbiopectobacterium, Sodalis, Serratia, and Tisiphia as candidate symbionts, with at least 16 independent acquisition events across the cimicid species, sometimes involving multiple strains per host. Phylogenetic comparisons indicated that some of these origins were followed by cospeciation. Wolbachia was present in most hosts except Cacodminae, where Symbiopectobacterium occurred as the sole symbiont, suggesting its obligate role. Analysis of 23 draft genomes revealed heterogeneity in size and gene content, consistent with varying stages of symbiotic reduction. Most lineages lost many biosynthetic pathways; only riboflavin and lipoic acid synthesis remained universally conserved. Our survey reveals a dynamic evolution of bed bug symbioses, with repeated symbiont acquisitions, cospeciation, and frequent coinfections. Despite independent origins, most symbionts belong to Wolbachia, Symbiopectobacterium, or Sodalis, implying unknown mechanisms shaping host specificity. Two points merit further study. First, Symbiopectobacterium as the sole obligate symbiont in Cacodminae suggests broader sampling may uncover greater symbiotic diversity. Second, uncertainties in biotin synthesis function call for deeper investigation into the evolution of this pathway in symbiotic bacteria.IMPORTANCEBed bugs are obligate blood-feeding insects that depend on bacterial partners to supply nutrients missing from their diet. Most previous research has focused on the human-associated species Cimex lectularius, leaving little known about symbiont diversity across other species. By surveying a broad phylogenetic range, we found that bed bugs have repeatedly acquired different bacteria as symbionts, including lineages not previously recognized as essential. Notably, finding Symbiopectobacterium as the sole symbiont in one subfamily shows that the nutritional partnerships in bed bugs are more dynamic than previously thought. At the same time, the majority of the 16 independent acquisitions involve only four bacterial genera, suggesting efficient mechanisms that constrain and shape bed bug-symbiont specificity.},
}

@article {pmid41211636,
year = {2025},
author = {Wu, L and Zhang, Q and Tang, Z and Li, Y and Wu, T and Chen, L and Tan, C and Zhang, L and Ji, X and Zhang, S and Wu, Y and Bozec, A and Zaiss, MM and Luo, Y},
title = {Gut microbiota-derived tryptophan indole metabolites ameliorate collagen-induced arthritis in mice via aryl hydrocarbon receptor activation in T cells and intestinal epithelial cells.},
journal = {Arthritis & rheumatology (Hoboken, N.J.)},
volume = {},
number = {},
pages = {},
doi = {10.1002/art.43430},
pmid = {41211636},
issn = {2326-5205},
abstract = {OBJECTIVE: To investigate the specific role of tryptophan metabolism, especially that of microbiome-derived metabolites, in the development of rheumatoid arthritis (RA).

METHODS: We employed metabolomics to profile metabolites in 53 high-risk for RA individuals (PreRAs), 30 established RA patients and 38 healthy individuals. Fecal microbiota transplantation (FMT) and collagen-induced arthritis (CIA) mouse models were used to investigate the impact of gut microbiome on arthritis severity, gut barrier function, and metabolic change. Treg cell differentiation and epithelial cells' barrier function were assessed by flow cytometry, immunofluoresence staining and western blotting. Co-immunoprecipitation and luciferase were applied for molecular mechanism studies.

RESULTS: Dysregulated tryptophan metabolism exists in RA and PreRA individuals, as well as in FMT mice, characterized by a shift toward the kynurenine pathway and reduced activity of serotonin and indole pathways. Indole-3-lactic acid (ILA) and indole-3-acetic acid (IAA) significantly alleviated arthritis in CIA mice by expanding Treg cells via the classical aryl hydrocarbon receptor (AhR)-aryl hydrocarbon receptor nuclear translocator (ARNT)-xenobiotic response element (XRE) signaling pathway. Moreover, ILA repaired the leaking gut by increasing Zo-1 and occludin expression in Caco-2 cells, which was blocked by AhR antagonist CH223191. Moreover, CH223191 treatment could significantly reverse the improving effects of ILA and IAA on arthritis in mice.

CONCLUSION: These findings indicate that Trp indole metabolites may play a negative regulatory role in the progression of RA by affecting Treg cell development and intestinal gut barrier function.},
}

@article {pmid41211602,
year = {2025},
author = {Wei, K and Yang, Y and Chen, C and Yang, Y and Hu, K and Chen, Q},
title = {Polypharmacy, anticholinergic burden and oral microbiome among U.S. middle-aged and older adults: a representative national survey.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2580559},
pmid = {41211602},
issn = {2000-2297},
abstract = {OBJECTIVES: Polypharmacy has been linked to alterations in gut microbiota, but its effects on the oral microbiome remain underexplored. This study aimed to examine the association of polypharmacy and anticholinergic burden with oral microbiome diversity and composition.

METHODS: We conducted a cross-sectional analysis using data from NHANES 2009-2012, including participants aged 55-69 years who reported at least one prescription medication. Polypharmacy was defined as the concurrent use of five or more medications. Anticholinergic burden was quantified by the Anticholinergic Cognitive Burden scale and the Anticholinergic Drug Scale. Oral microbiome profiling comprised alpha diversity, beta diversity, and taxonomic composition at multiple phylogenetic levels. Associations were analyzed via weighted multivariable linear regression, principal coordinate analysis (PCoA), and multivariate analysis of variance.

RESULTS: Among 1,596 participants, 29.2% reported polypharmacy, which correlated with higher anticholinergic burden. Both polypharmacy and anticholinergic burden were inversely associated with alpha diversity across multiple measures. Taxonomic analyses showed heterogeneous associations, with Porphyromonadaceae negatively linked to both exposures. PCoA indicated significant differences in community structure by polypharmacy status (Bray-Curtis: R² = 0.35%, P < .001).

CONCLUSIONS: Among middle-aged and older U.S. adults, both polypharmacy and anticholinergic burden were inversely associated with oral microbiome diversity and linked to distinct microbiome composition.},
}

@article {pmid41211554,
year = {2025},
author = {Gwon, H and Kim, HJ and Jeong, JW and Lee, D and Kim, JY and Shim, JJ and Lee, JH},
title = {Therapeutic potential of Codonopsis lanceolata peel extract in premenstrual syndrome: insights into hormonal, immune, and microbial interactions.},
journal = {Food science and biotechnology},
volume = {34},
number = {16},
pages = {4027-4038},
pmid = {41211554},
issn = {2092-6456},
abstract = {UNLABELLED: This study investigated the therapeutic potential of Codonopsis lanceolata peel extract (CPE) for premenstrual syndrome (PMS). The focus was on hormonal, immune, and microbial pathways. In vitro, CPE reduced nitric oxide production and suppressed IL-6 and TNF-α expression in LPS-stimulated macrophages. In pituitary GH3 cells stimulated with estradiol, CPE inhibited prolactin secretion. In a metoclopramide (MCP)-induced hyperprolactinemia mouse model, CPE decreased serum prolactin, PGE2, and inflammatory cytokines, while increasing PGE1 and FSH levels. Microbiome analysis showed that CPE enriched beneficial genera such as Lactobacillus and Bifidobacterium and reduced pro-inflammatory taxa including Oscillibacter and Desulfovibrionaceae. These microbial shifts were associated with improved inflammatory and hormonal markers. Overall, these findings suggest that CPE alleviates PMS symptoms by modulating endocrine function and regulating gut microbiota.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10068-025-02003-w.},
}

@article {pmid41211371,
year = {2025},
author = {Fang, L and Herrera-Herrera, A and Harris-Ricardo, J and Olier-Castillo, D and Fortich-Mesa, N and Hoyos-Hoyos, V},
title = {Exploring the Oral Microbiome in the Dental Biofilm of Children with Caries from Vulnerable Communities in Cartagena, Colombia: A Cross-sectional Study.},
journal = {International journal of clinical pediatric dentistry},
volume = {18},
number = {10},
pages = {1211-1216},
pmid = {41211371},
issn = {0974-7052},
abstract = {AIMS AND BACKGROUND: To explore the oral microbiome in the cariogenic dental biofilm in children from vulnerable communities in Cartagena, Colombia.

MATERIALS AND METHODS: We conducted a prevalence study that included 75 children aged 5-8 from three vulnerable communities in Cartagena, Colombia. Taking into account the International Caries Detection and Assessment System (ICDAS), calibrated examiners diagnosed all participants with dental caries. Samples of dental biofilm were obtained from carious tooth surfaces; extraction of bacterial DNA (deoxyribonucleic acid) was performed, and sequenced V3-V4 region of 16S rRNA (ribosomal ribonucleic acid) gene. Statistical analyses were conducted at the genus and species levels. Microbial diversity was analyzed using the Shannon diversity index.

RESULTS: The most prevalent bacterial genera identified were Streptococcus (probe 4), Lactobacillus (probe 5), Streptococcus (probe 1), and Fusobacterium (probe 4). The most abundant species identified were Lactobacillus salivarius, Streptococcus mutans, Streptococcus sanguinis, and Leptotrichia sp. HOT 417. A comparison of relative species abundance showed a more significant presence of Parascardovia denticolens, S. mutans, and Streptococcus sobrinus in extensive cavitated carious lesions (p < 0.001). The oral biofilm exhibited richness in bacterial species, as the α-Shannon index of 3.02 (SD 0.36) indicated.

CONCLUSION: The oral microbiome in the cariogenic dental biofilm in children from vulnerable communities in Cartagena shows high bacterial diversity, with specific species significantly associated with extensive cavitated lesions.

CLINICAL SIGNIFICANCE: Understanding the microbial diversity and specific bacterial associations in carious lesions provides valuable insights for developing targeted preventive and therapeutic strategies.

HOW TO CITE THIS ARTICLE: Fang L, Herrera-Herrera A, Harris-Ricardo J, et al. Exploring the Oral Microbiome in the Dental Biofilm of Children with Caries from Vulnerable Communities in Cartagena, Colombia: A Cross-sectional Study. Int J Clin Pediatr Dent 2025;18(10):1211-1216.},
}

@article {pmid41211322,
year = {2025},
author = {Pires, CP and Villela, LB and Moura, RL and Salomon, PS and Silva-Lima, AW},
title = {Hidden microalgae diversity in reef systems: reanalysis of coral microbiomes reveals spatial patterns of coral-associated plastid communities in the Southwestern Atlantic Ocean (SWAO).},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20116},
pmid = {41211322},
issn = {2167-8359},
abstract = {The microbial community associated with corals plays a critical role in reef ecosystems, yet studies mainly focus on prokaryotes and Symbiodiniaceae, overlooking other oxygen-evolving photosynthetic eukaryotes. This leaves a knowledge gap regarding potentially important microbiome members. Here, we revisited coral microbiome datasets to investigate the diversity of plastid-bearing eukaryotes associated with Southwestern Atlantic Ocean (SWAO) corals. We compiled an inventory of plastid-bearing communities, uncovering their diversity and exploring ecological patterns. We further applied this approach to analyze the plastidiomes (plastid-bearing communities) of corals from the Abrolhos Bank, the largest reef system in the region, as a case study. A systematic literature review of 16S rDNA-based coral microbiome was conducted, excluding studies lacking plastid 16S sequences. The search made in PubMed resulted in 19 studies reporting corals sampled from 2009 to 2022, which were compiled and reanalyzed. Sequences of chloroplast origin (Silva 132) were further taxonomically classified by consensus-BLASTn search with the PR2 plastid 16S database. The dataset encompassed reef water and coral microbiomes from eight coral species, emphasizing the genus Mussismilia. A total of 272 amplicon libraries yielded 707,949 plastid sequences, identifying 196 algal genera across 41 classes. Reef water and coral plastid communities differed markedly. Ostreobium (81%) and Calliarthron (49%) were the most prevalent genera in coral samples. Diatoms were common (>40% of samples) in the water and in corals, whereas corallicolids were exclusive to corals (31.8%). The Abrolhos case study revealed geographic variation in Mussismilia harttii plastidiomes, which were less diverse than those in the water column. Coral indicator taxa included Ostreobium, corallicolids, Navicula, and Amphora. Our findings identify plastidiome variations and their implications for the coral host. Lipid-rich diatoms prevalent in coral plastidiomes may support corals nutritionally after coral bleaching, while other free-living and bloom-forming microalgae produce significantly more reactive oxygen species than Symbiodiniaceae, potentially driving oxidative stress. These results highlight microeukaryotic community variation across corals and its ecological relevance, offering a framework for using plastid-bearing communities as biomarkers of shifts in coral holobionts.},
}

@article {pmid41211308,
year = {2025},
author = {Delitte, M and Dubois, B and Morandini, L and Bultreys, A and Mahillon, J and Debode, F and Bragard, C},
title = {Biocontrol-relevant diversity of wheat-associated Pseudomonas: prevalence of P. sivasensis and identification of the novel species P. arvensis sp. nov.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20177},
pmid = {41211308},
issn = {2167-8359},
abstract = {The role of microbial communities in plant health and productivity has become increasingly evident. In this study, we investigated the diversity and functional potential of Pseudomonas spp. associated with Belgian cereal crops, focusing on wheat and spelt. From 444 Pseudomonas isolates, we identified 11 species, with several strains exhibiting strong antagonistic activity against major wheat pathogens. Notably, we report the high prevalence and efficient colonization abilities of Pseudomonas sivasensis, including its capacity to translocate from seed to leaf and suppress Zymoseptoria tritici infection in planta. Furthermore, we describe Pseudomonas arvensis sp. nov., a newly characterized species within the wheat microbiome, with DR1PS3 designated as the type strain. Our results advance the understanding of beneficial plant-microbe interactions in cereals and highlight the promise of native Pseudomonas species as biocontrol agents for sustainable disease management.},
}

@article {pmid41210947,
year = {2025},
author = {Negut, I and Mazzanti, C and Laurano, R and Ciardelli, G and Bronco, S and Oliveira, CS},
title = {From 1D microbiological assays to 3D advanced skin models: enhancing preclinical strategies to unravel the impact of bioactive textiles on the human skin microbiome.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1676663},
pmid = {41210947},
issn = {2235-2988},
abstract = {Bioactive textiles have emerged as multifunctional materials to actively interact with the human skin and its microbiome. By embedding natural or synthetic bioactive compounds, such as chitosan, essential oils, plant extracts, and metallic nanoparticles, these materials aim to prevent and target infections, modulate inflammation, and promote skin homeostasis. Given the critical role of the skin microbiome in maintaining barrier integrity and immune balance, strategies that selectively inhibit pathogenic microorganisms (e.g., Staphylococcus aureus, Cutibacterium acnes) while preserving beneficial commensals like Staphylococcus epidermidis are essential to avoid dysbiosis and associated dermatological disorders. This review highlights current trends in the design and functionalization of bioactive textiles, emphasizing sustainable and biocompatible approaches that leverage natural antimicrobial compounds and green synthesis techniques. It also examines conventional evaluation pipelines primarily based on 1D microbiological assays and 2D skin models, highlighting their limitations in predicting real-world performance. Advanced in vitro models, particularly 3D reconstructed human skin platforms incorporating both pathogenic and commensal microbiota members, are presented as indispensable tools to study fabric-skin-microbe interactions under physiologically relevant conditions. These models enable accurate assessment of antimicrobial efficacy, biocompatibility, and microbiome impact, providing a bridge between in vitro and clinical outcomes. Furthermore, the potential of bioactive textiles in managing microbiome-related skin conditions, such as atopic dermatitis and acne, is discussed alongside the importance of developing microbiome-safe materials. Despite encouraging clinical evidence demonstrating pathogen reduction and symptomatic improvement, the successful translation of these materials to clinical practice needs interdisciplinary research and the adoption of advanced preclinical strategies to ensure innovative solutions for personalized skin health.},
}

@article {pmid41210709,
year = {2025},
author = {Hou, L and Han, B and Wang, Y and Wang, X and Shi, W and Cao, N and Zhang, Y},
title = {Microbial response to long-term spatially stratified phosphorus application in Northeast China.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1669876},
pmid = {41210709},
issn = {1664-462X},
abstract = {As a critical factor influencing crop productivity in agricultural ecosystems, phosphorus (P)-fertilizer application can significantly alter soil physicochemical properties. However, the relative efficiencies of different types of spatially stratified P fertilizers and their underlying biological mechanisms remain insufficiently elucidated. In this study, an 8-year field experiment was conducted in a black soil region of Northeast China to compare the effects of five P-fertilization regimes: CK (without P application), FP (100% as basal fertilizer), APP (20% as starter fertilization by ammonium polyphosphate), MAP (20% as starter fertilization by monoammonium phosphate), and CMP (20% as starter fertilization by calcium magnesium phosphate). We systematically investigated the effects of spatially stratified P fertilization on soil physical properties, nutrient accumulation, maize yield performance, and bacterial and fungal community structure. CMP demonstrated the best performance in improving soil aeration and enhancing water infiltration capacity. MAP significantly increased the soil total P content by 18.62% and the soil Olsen-P content by 81.46% compared to those of FP. Both MAP and CMP promoted P uptake in various parts of maize plants, including the roots, straw, and grains. All tested starter P fertilizers improved P use efficiency. Compared to that of FP, the soil P surplus was reduced by 7.52%, 14.74%, and 13.04% under APP, MAP, and CMP, respectively. MAP demonstrated the most pronounced yield-increasing effect. Based on amplicon sequencing (16S rRNA for bacteria, interspacer region for fungi) and microbiome profiling, this study confirms that fungi are more susceptible than bacteria to variations in fertilizer types and application methods. Furthermore, the relative abundance of Tausonia was most significantly influenced by MAP. By enhancing the relative abundance of P-cycling functional genes (gph, phoU), MAP modulated the abundance of dominant microbial taxa such as Acidobacteria and Proteobacteria, thereby significantly improving maize yield. Therefore, in maize cropping systems in the black soil region of Northeast China, optimized P fertilizer selection and application methods can effectively reduce soil P surplus and modulate microbial community structure and functional diversity while maintaining stable crop yields.},
}

@article {pmid41210228,
year = {2025},
author = {Huang, H and Ma, D and Zhou, Y and Wu, L},
title = {Effect of probiotics and related supplements on glycemic control in pediatric patients with type 1 diabetes mellitus: a systematic review and meta-analysis of clinical trials.},
journal = {Frontiers in pediatrics},
volume = {13},
number = {},
pages = {1633694},
pmid = {41210228},
issn = {2296-2360},
abstract = {OBJECTIVE: Type 1 diabetes mellitus (T1DM) is a common autoimmune disease in children, characterized by the destruction of pancreatic β-cells. Despite treatment advancements, many patients struggle with glycemic control. Recent research suggests the gut microbiome plays a role in T1DM, with dysbiosis contributing to its onset. Probiotics may help improve glycemic control and reduce inflammation, but their effects in children with T1DM are unclear. This study systematically reviews the impact of probiotics and related supplements on glycemic control in pediatric T1DM patients.

METHODS: This study adhered to PRISMA guidelines and was registered in PROSPERO (CRD42025633971). We searched databases including PubMed and EMBASE until January 5, 2025. The focus was on randomized controlled trials (RCTs) involving participants under 18 with T1DM, examining the effects of probiotics, prebiotics, and synbiotics on glycemic control indexes like fasting blood glucose (FBG), hemoglobin A1c (HbA1c), C-peptide, and insulin needs. Two researcher extracted data, quality was assessed via the Cochrane Handbook, and STATA 16 was used for statistical analysis.

RESULTS: Eight RCTs with 494 participants (246 intervention, 248 control) showed that probiotics and synbiotics significantly reduced HbA1c levels [Weighted Mean Difference (WMD) = -0.25%, 95% Confidence Interval (CI) = -0.45, -0.04; p = 0.019] with low heterogeneity [I-squared (I[2]) = 22%]. However, no significant changes were found in FBG, C-peptide levels, or insulin requirements. Sensitivity analyses yielded similar directions of effect for HbA1c. Subgroups suggested larger HbA1c reductions with longer intervention duration, shorter disease duration, and multi-strain formulations.

CONCLUSION: Probiotic supplementation may achieve a small improvement in HbA1c in pediatric T1DM. Adequate dosing, longer intervention duration, and multi-strain formulations may be more likely to improve HbA1c, but the clinical importance is uncertain. However, our result shows no significant effects on fasting blood glucose, C-peptide, or insulin requirements; no routine clinical recommendations are proposed. The role of probiotics and related supplements in long-term glycemic control still requires confirmation through trials with extended follow-up. Large-scale, rigorously designed studies are needed to determine optimal intervention parameters, clarify underlying mechanisms, and evaluate the clinical applicability of probiotics in T1DM management.

identifier [CRD42025633971].},
}

@article {pmid41209829,
year = {2025},
author = {Yang, M and Liu, Y and Xia, Y and Li, M and Huang, C and Hou, F and Hu, S and Zhu, X and Wang, M and Shi, J and Wan, R and Zhang, K and Hao, P and Zhao, Y and Liu, Y and Shen, Y and Cong, L and Han, Z and Feng, J and Jiao, J and Zheng, X},
title = {A synthetic microbial community derived from healthy apple rhizosphere alleviates apple replant disease.},
journal = {Horticulture research},
volume = {12},
number = {11},
pages = {uhaf217},
pmid = {41209829},
issn = {2662-6810},
abstract = {Apple replant disease (ARD) poses a major threat to global orchard productivity, yet its biological causes remain poorly understood. Although microbial dysbiosis in replant soils has been recognized as a major contributing factor, the specific pathogenic agents involved and the efficacy of synthetic microbial communities in mitigating ARD remain unclear. In this study, we integrated physiological, transcriptomic, metabolomic, and microbiome analyses to investigate the effects of replant soils on the growth of Malus domestica rootstock M26. Absolute quantification amplicon sequencing of 16S rRNA and ITS regions revealed a marked decline in rhizospheric microbial diversity in replant soils compared to fallow controls, accompanied by an enrichment of fungal genera such as Fusarium, Aspergillus, and Acremonium. Pathogenicity assays and seedling colonization experiments verified strong pathogenicity for five isolates-Acremonium sp., Aspergillus niger, Fusarium solani, Macrophomina phaseolina, and Aspergillus stellatus-implicating them as potential causal agents of ARD. High-throughput culturing and confrontation assays were used to isolate and screen candidate microbial antagonists. A synthetic microbiota (SynMs) composed of 12 bacterial strains and Trichoderma sp. was developed. Inoculation with SynMs significantly inproved plant height by 133% (P < 0.05) and total root length by 186% (P < 0.01), and effectively suppressed pathogen proliferation of the five pathogenic isolates in replant soils. Collectively, these findings identify key fungal pathogens underlying ARD and propose a sustainable microbiota-based strategy for its effective mitigation, offering both mechanistic insights and practical solutions for microbiome-informed orchard management.},
}

@article {pmid41209726,
year = {2025},
author = {Sun, Z and Huang, R and Chen, J and Song, Y and Sun, Z and Zhang, L and Shi, H and Mu, R and Wang, Y and Huang, J and Yan, X and Tan, Q},
title = {Androgen deprivation promotes diabetic wound healing in mice through modulation of wound microbiome and immune response.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1684165},
pmid = {41209726},
issn = {1664-302X},
abstract = {INTRODUCTION: Delayed wound healing is a major complication of diabetes, often associated with chronic inflammation and microbial dysbiosis. Although androgens are known to impair wound repair, their role in diabetic wound healing, particularly in regulating the local wound microbiome and associated immune response, remains poorly understood. In this study, we investigated whether androgen deprivation via surgical castration could enhance diabetic wound healing by modulating local microbial communities and inflammation.

METHODS: A full-thickness wound model was established in db/db mice. Surgical castration was used to achieve androgen deprivation. Wound closure and histology were assessed longitudinally. Blood glucose and body weight were monitored. The local immune microenvironment was profiled, focusing on pro-inflammatory factors and macrophage polarization. 16S rRNA sequencing characterized α-diversity and community composition over time. Functional prediction analyses inferred microbial metabolic potential, and machine-learning models evaluated taxa associated with healing dynamics.

RESULTS: Androgen deprivation significantly accelerated wound closure and improved histological outcomes without altering blood glucose or body weight. The wound microenvironment showed reduced pro-inflammatory factors and enhanced M2 macrophage polarization. 16S rRNA sequencing revealed increased microbial α-diversity and durable shifts in community composition, most prominently during early healing. Escherichia-Shigella, Rhodococcus, and Ochrobactrum were enriched, while Staphylococcus abundance decreased. Functional prediction indicated elevated microbial metabolic activity after castration. Machine-learning analysis identified Escherichia-Shigella as a key genus associated with accelerated healing.

DISCUSSION: Low androgen levels were associated with improved diabetic wound repair, potentially by attenuating local inflammation and fostering a more diverse, metabolically active microbiota. These data support a mechanistic link among androgens, wound inflammation, and the microbiome, and suggest host-directed therapeutic strategies for chronic diabetic wounds.},
}

@article {pmid41209719,
year = {2025},
author = {Tufail, A and Bo, T and Zhao, N and Willows-Munro, S and Khan, BN and Duan, J and Jin, J and Qu, Y and Lei, F and Song, G},
title = {Exploring microbiome shifts across taxonomic and ecological groups of birds at a key stopover site in Punjab, Pakistan.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100492},
pmid = {41209719},
issn = {2666-5174},
abstract = {Birds are important vectors of microbial transmission across diverse habitats. yet their gut microbiome dynamics from South Asian migratory stopover sites remain poorly understood. This study presents the first comprehensive assessment of gut microbiome variation across avian ecological types during the late wintering period at the Ravi River Siphon, a stopover in Punjab, Pakistan. Using 16S rRNA gene sequencing, we profiled gut microbial characters of 41 bird individuals from 17 species representing seven avian orders. Alpha diversity differed significantly across both ecological types and taxonomic orders, while beta diversity showed overlapping communities, with limited group distinctions. Dominant phyla included Firmicutes, Proteobacteria, Actinobacteriota, Chloroflexi, and Bacteroidota, with notable group specific enrichments. LEfSe analysis identified five differentially abundant biomarker taxa across ecological types and seven orders, and PICRUSt2 based functional predictions revealed enrichment of pathways related to metabolism, immune function, and xenobiotic degradation, varying notably by ecological type/taxonomic orders. Importantly, we detected several potential zoonotic pathogens, including Enterococcus, Escherichia-Shigella, Acinetobacter, and Corynebacterium, highlighting the need for pathogen surveillance in avian populations. Our findings indicate that both ecology and host taxonomy are key determinants of avian gut microbiome composition, with taxonomic order showing a stronger influence on microbial structure. Together, these results provide the first region-specific baseline from a migratory stopover in Punjab, Pakistan, addressing a major geographic gap in avian microbiome research and offering essential data for future conservation and pathogen monitoring in dynamic wetland ecosystems.},
}

@article {pmid41209469,
year = {2025},
author = {Zhao, Z and Wei, X and Deng, F and Yang, S and Li, Y and Chai, J},
title = {Editorial: Advancements in synthetic microbiomes for enhancing animal health.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1708299},
pmid = {41209469},
issn = {2297-1769},
}

@article {pmid41209147,
year = {2025},
author = {Massey, WJ and Brown, JM},
title = {The role of metaorganismal lipid metabolism in human health and disease.},
journal = {Immunometabolism (Cobham, Surrey)},
volume = {7},
number = {4},
pages = {e00074},
pmid = {41209147},
issn = {2633-0407},
abstract = {Most chronic diseases including coronary heart disease, obesity, diabetes, cancer, and multiple neurodegenerative diseases are driven by dysregulated lipid metabolism. In fact, many common drugs taken by millions including aspirin, statins, fibrates, and others improve health by reorganizing systemic lipid metabolism. Although we have a wealth of information on the enzymes and pathways maintaining lipid metabolic homeostasis in our human cells, there is much less known in regard to how our gut microbiome may coordinate with the host to control systemic lipid metabolism. With advances in untargeted metabolomics, there is a rapidly expanding list of gut microbe-derived lipid metabolites with unannotated function. Many of these bacterial lipids can be assimilated into host lipids and alter host lipid metabolic processes. Here, we discuss how gut microbe-derived lipids may be further metabolized by the host through metaorganismal metabolic pathways. We also discuss the untapped therapeutic potential for targeting metaorganismal lipid metabolism for the improvement of human health.},
}

@article {pmid41209022,
year = {2025},
author = {Piednoir, A and Troussier, F and Descamps, M and Lagarce, L and Martin, L},
title = {Cutaneous and Ocular Rosacea Associated with Elexacaftor, Tezacaftor and Ivacaftor, A Treatment for Cystic Fibrosis: A Case Report.},
journal = {Journal of pediatrics. Clinical practice},
volume = {18},
number = {},
pages = {200187},
pmid = {41209022},
issn = {2950-5410},
abstract = {A 6-year-old girl with cystic fibrosis developed ocular and cutaneous rosacea after the initiation of elexacaftor-tezacaftor-ivacaftor therapy. Her symptoms improved upon discontinuation and recurred with reintroduction, suggesting a drug-induced reaction. This case suggests a potential, previously unreported association between elexacaftor-tezacaftor-ivacaftor and rosacea, possibly mediated by microbiome alterations and inflammation.},
}

@article {pmid41208900,
year = {2025},
author = {Yang, R and Yang, Y and Wu, L and He, K and Bi, D and Teng, L},
title = {Lactobacillus paracasei ZJUZ2-3 inhibits gastrointestinal tumors via the IAA-induced AHR/MTDH/NF-κB axis.},
journal = {International journal of biological sciences},
volume = {21},
number = {14},
pages = {6522-6541},
pmid = {41208900},
issn = {1449-2288},
abstract = {Lactobacillus paracasei abundance is markedly reduced in gastric cancer (GC) tissues, suggesting its potential protective role. From healthy gastric tissue of a GC patient, we isolated a novel strain, L. paracasei ZJUZ2-3, which exerted potent antitumor effects. Intratumoral injection of live ZJUZ2-3, but not heat-killed bacteria, attenuated gastrointestinal tumor growth in mice. Conditioned medium from ZJUZ2-3 similarly inhibited cancer cell proliferation, implicating a secreted metabolite. Metabolomic profiling identified indole-3-acetic acid (IAA) as the key bioactive compound. Consistent with this, genetic knockout of trpA (essential for IAA biosynthesis) in ZJUZ2-3 abolished its antitumor efficacy. IAA alone recapitulated the tumor-suppressive effects both in vitro and in vivo. Mechanistically, IAA activated the aryl hydrocarbon receptor (AHR), which then competitively bound to metadherin (MTDH). This interaction blocked MTDH phosphorylation and the subsequent activation of NF-κB signaling. Crucially, depletion of either AHR or MTDH abrogated IAA's efficacy, underscoring the essential role of this axis. Furthermore, ZJUZ2-3 synergized with conventional chemotherapy, potentiating tumor regression. While this study lacks humanized immune models and exploration of strain-specificity, our findings identify L. paracasei ZJUZ2-3 and its effector metabolite IAA as promising precision microbiome-based therapeutics targeting the AHR-MTDH-NF-κB pathway for adjuvant treatment of GC.},
}

@article {pmid41208872,
year = {2025},
author = {Sun, J and Chen, J and Shen, Y and Yao, X and Sun, H and Chen, B and Feng, J},
title = {Diabetes mellitus-driven pulmonary injury: multidimensional mechanisms linking metabolic dysregulation to gut-lung axis and promising therapies.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1689522},
pmid = {41208872},
issn = {1663-9812},
abstract = {Diabetes mellitus (DM), a globally prevalent metabolic disorder, poses a significant public health threat due to its systemic complications. Recent studies have increasingly recognized the lung as a target organ in diabetic pathology. However, owing to the respiratory system's complex physiology, the mechanisms underlying DM-associated lung injury remain poorly understood and require further investigation. This review systematically elucidates the multifaceted effects of DM-induced metabolic disturbances on the lung, with a focus on four key pathophysiological axes triggered by hyperglycemic homeostasis, including chronic inflammation, oxidative stress imbalance, endocrine network disruption, and intestinal dysbiosis. Building upon the "metabolism-microbiota-immune" axis framework, this study demonstrates that: persistent hyperglycemia induces pulmonary tissue damage and immune microenvironment disruption through metabolite accumulation and mitochondrial dysfunction; DM-associated intestinal dysbiosis amplifies pulmonary inflammation via the gut-lung axis, mediated by metabolic reprogramming and immune cell trafficking; and metabolic aberration-driven dysregulation of innate/adaptive immunity serves as the pivotal mediator for progressive lung injury. Building on this mechanistic framework, we discuss emerging therapeutic avenues that target metabolic reprogramming, modulation of the gut microbiota, and restoration of immune homeostasis. Promising strategies include repurposed antidiabetic drugs (e.g., SGLT-2 inhibitors, GLP-1 receptor agonists), microbiome-targeted therapies (e.g., fecal microbiota transplantation), and novel immunomodulatory agents. These therapies are offering a new shift towards multi-target treatments for diabetic pulmonary complications.},
}

@article {pmid41208518,
year = {2025},
author = {Yang, Y and Wen, L and Lin, W and Chen, Y and Yang, R and He, C and Zhang, Y and Zhang, J and Wang, H and Wang, H and Teng, L},
title = {Microbial and Metabolomic Variations Correlated With Gastric Cancer Subtypes and Prognosis.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70139},
doi = {10.1002/mbo3.70139},
pmid = {41208518},
issn = {2045-8827},
support = {//This study was supported by the National Natural Science Foundation of China (No. 82302886), the Project of the Regional Diagnosis and Treatment Centre of the Health Planning Committee (No. JBZX-201903), and the Department of Science and Technology of Zhejiang Province, "Pioneer" and "Leading Goose" R&D Program of Zhejiang, NO.2024C03146./ ; },
abstract = {Gastric cancer (GC) persists as the third most prevalent malignancy in China. GC exhibits distinct features when stratified by Lauren/ZJU subtypes. The interdependence of microbes, metabolites, and tumor evolution is recognized. Nevertheless, the specific microbial and metabolite disparities related to the Lauren and ZJU subtypes of GC have yet to be thoroughly investigated. In this study, we employed 16S sequencing of microbial communities and conducted untargeted metabolomic assessments on tumor tissues and their matched normal controls from 50 GC patients. We observed variations in microbial composition and metabolite landscapes across subtypes, irrespective of the Lauren or ZJU classification. We explored the associations and differences between the Lauren and the ZJU classification. It was found that both classifications share differential microbiota, including Fusobacterium and Haemophilus. Additionally, 38 of the top 50 differential metabolites are common to both classifications. However, distinct classifications also exhibit unique differential microbiota and metabolite characteristics. Among them, Eubacterium_ventriosum_group and N6-Succinyl Adenosine are both characteristic differences of the ZJU classification. Multivariate survival analysis disclosed that Eubacterium_ventriosum_group positively correlates with poor prognosis, whereas N6-Succinyl Adenosine negatively correlates with poor prognosis. Our research delineates the microbiota and metabolites specific to different subtypes of GC and investigates the interplay between these differential elements, as well as their prognostic significance. We have identified two distinct features that are both associated with the ZJU classification, suggesting that the ZJU classification is more closely related to prognosis.},
}

@article {pmid41208300,
year = {2025},
author = {Ma, Y and Yan, H and Abukhader, OS and Li, D and Zhang, S},
title = {Sublethal effects of matrine and azadirachtin on the wolf spider Pardosa laura: no impairment of growth but marked suppression of reproduction.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.70347},
pmid = {41208300},
issn = {1526-4998},
support = {//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Plant-derived pesticides (PDPs) are increasingly promoted as 'eco-friendly' alternatives to agrochemicals because of their low vertebrate toxicity, yet their safety for non-target arthropod natural enemies is rarely tested, especially the enrichment effect via trophic transfer.

RESULTS: We cultured fruit flies using media supplemented with two widely applied Chinese PDPs in tea plantations, matrine or azadirachtin, under commercial concentration, which were fed to newly emerged spiderlings of wolf spider Pardosa laura (Araneae: Lycosidae) throughout their entire life cycle. We examined the effect of these two PDPs on their survival, developmental parameters and reproduction. The results showed that developmental traits remained unaffected, but both PDPs markedly suppressed male mating success and female fecundity. Histological examination of paraffin sections revealed markedly impaired ovarian maturation. Microbiome profiling indicated that pesticide exposure disrupted ovarian microbial communities, with azadirachtin exerting the strongest effect, whereas gut and testicular communities remained largely unchanged. Transcriptomic analysis of ovaries showed significant enrichment of pathways related to ovarian development. Ten representative differentially expressed genes (DEGs) within these pathways were selected and validated by RT-qPCR.

CONCLUSION: PDPs may not compromise the development of spiders in the first generation, yet they can severely affect reproduction of the spiders, thereby precipitating substantial declines in population size of future generations. This result challenges the conventional wisdom of botanical pesticides, inspiring re-consideration of their rational use in integrated pest management. © 2025 Society of Chemical Industry.},
}

@article {pmid41208257,
year = {2025},
author = {Dias Nirello, V and Araújo, N and Carvalho de Assis, H and Moreno-Gonzalez, M and Ruiz, P and Castro, PR and Shealy, NG and Shelton, C and Font Fernandes, M and de Oliveira, S and Boroni, M and Ryffel, B and Byndloss, MX and Beraza, N and Ramirez Vinolo, MA and Varga-Weisz, P},
title = {Microbiota shape the colon epithelium controlling inter-crypt absorptive goblet cells via butyrate-GP R109A signalling.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2573045},
doi = {10.1080/19490976.2025.2573045},
pmid = {41208257},
issn = {1949-0984},
abstract = {The colonic epithelium is a key interface between the gut microbiota and the host. How microbiota-derived signals influence epithelial cell identity and function remains incompletely understood. Here, we used single-cell transcriptomics, antibiotic-mediated microbiota depletion, germ-free mice and colonization experiments in mice to uncover cell-type-specific responses to microbiota changes, highlighting changes in the cell composition and functional diversities in enterocytes. Our analysis demonstrates that the microbiota control the absorptive profile of the colon epithelial cells and reveals non-canonical inter-crypt goblet cells as microbiota-responsive constituents that combine absorptive and secretory features and whose abundance is regulated by the gut microbiota. We found that their number is suppressed through the short-chain fatty acid butyrate and its receptor GPR109A. Analysis in mouse and humans indicates that the expansion of this hybrid population increases with age and that this expansion is driven by microbiome changes. Our work reveals a previously unrecognized level of epithelial plasticity driven by microbial triggers and highlights butyrate, acting as a signaling molecule that shapes the colon micro-anatomy.},
}

@article {pmid41208251,
year = {2025},
author = {Ding, M and Ross, RP and Dempsey, E and Li, B and Stanton, C},
title = {Infant gut microbiome reprogramming following introduction of solid foods (weaning).},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2571428},
doi = {10.1080/19490976.2025.2571428},
pmid = {41208251},
issn = {1949-0984},
abstract = {The infant gut microbiome undergoes a crucial transformation when solid foods enter the diet during weaning. This introduction normally happens at about six months post-birth and leads to major shifts in the gut microbiome. Many of the changes that occur during this period are known to persist into adulthood. While many perinatal factors, including gestational age, delivery mode, feeding choices, and antibiotic exposure, strongly influence microbiome composition and functional trajectories, the effects of weaning, in particular, have received far less attention. This review examines the response of the microbiome ecosystem when the diet is radically altered through the introduction of solid foods during the weaning phase. This response involves major reshaping of anabolic and catabolic functioning, along with changes in bacterial taxa and increased diversity. The information presented in this review aims to fill existing knowledge gaps while advancing our comprehension of how the infant diet shapes gut microbiome development through childhood.},
}

@article {pmid41207985,
year = {2025},
author = {Mei, J and Li, L and Ma, ZS},
title = {Unraveling the Ecological Mechanisms Influencing the Structure and Composition of Lung Cancer Microbiomes.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {119},
pmid = {41207985},
issn = {1432-184X},
abstract = {This study investigates the ecological mechanisms governing the structure and composition of lung microbiome communities within tumor tissue from lung cancer patients. While this field has attracted increasing research attention, the ecological and etiological mechanisms driving microbial community assembly in this environment remain poorly characterized. To address this gap, we applied Sloan's near neutral model, Ning et al.'s normalized stochasticity ratio framework and Harris et al.'s multi-site neutral model to evaluate the influences of stochastic and deterministic factors at species, community and metacommunity levels, respectively. Our findings include: (i) Stochastic drift exhibited predominant influence at both species and community levels in normal adjacent tissue (NT), exceeding its effects in LUAD (lung adenocarcinoma) and LUSC (lung squamous cell carcinoma). (ii) At the metacommunity level, neutrality was not rejected at the metacommunity or local community levels, which is consistent with the previous finding (i). (iii) Elevated metacommunity biodiversity (θ) and immigration rates (m) in LUAD/LUSC compared to NT (observed in ∼50% of cases) suggest that tumor occurrence/progression may actively promote microbial recruitment to tumor microenvironments. We propose three non-exclusive mechanistic interpretations: (i) Tumor-mediated immune modulation creates permissive ecological niches; (ii) structural remodeling of tissue enhances microbial colonization potential; (iii) selective enrichment of opportunistic taxa (e.g., Streptococcus) through tumor-specific microenvironmental changes. Our results demonstrate that LUAD and LUSC microbiomes are shaped by deterministic tumor-driven selection, in contrast to the predominantly stochastic assembly observed in NT microbiomes. These findings reveal substantial reorganization of tumor-associated microbial communities, warranting further biomedical investigation and clinical validation.},
}

@article {pmid41207977,
year = {2025},
author = {Oliveira-Pinto, PR and Oliveira-Fernandes, J and Gramaje, D and Santos, C},
title = {Metabarcoding Profiling Reveals Microbiome Structure and Predicts Functional Shifts in Grapevines Challenged by Phyllosticta ampelicida.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {120},
pmid = {41207977},
issn = {1432-184X},
abstract = {Black rot disease (BRD), caused by the still understudied Phyllosticta ampelicida, is spreading across several grape producing countries, posing a growing threat to the agroindustry. The role of the grapevine microbiome in defending against this pathogen, particularly in terms of microbiota structure and community homeostasis, remains unclear. In this study, we aimed to characterize the epiphytic phyllosphere microbiota of grapevines and identify shifts in microbial genetic structure associated with BRD symptoms. We sampled three vineyards of the cultivar "Touriga Nacional" in the Douro region (Portugal), collecting 20 leaves from (a) five healthy and (b) five BRD-symptomatic grapevines. The presence of P. ampelicida was confirmed in all symptomatic samples. Epiphytic bacterial DNA was extracted and sequenced using next-generation sequencing (NGS). Results indicate that although overall the diversity and richness indexes were not different in diseased plants compared to healthy ones, there was a reduction in OTU richness in black rot-affected grapevines. Diseased plants exhibited significant shifts in microbial network assemblages and showed an increased relative abundance of certain taxa, such as Acinetobacter, suggesting a possible recruitment of beneficial bacteria in response to biotic stress. Additionally, we observed a higher abundance of antibiotic resistance-related KEGG Orthologues (KOS) in symptomatic plants, raising potential concerns for human health. This study presents the first characterization of the grapevine phyllosphere epiphytic bacterial microbiota and its structural shifts in response to BRD.},
}

@article {pmid41207775,
year = {2026},
author = {Belzer, A and Coates, SJ},
title = {Climate Change and Infectious Diseases in Dermatology.},
journal = {Dermatologic clinics},
volume = {44},
number = {1},
pages = {45-65},
doi = {10.1016/j.det.2025.08.003},
pmid = {41207775},
issn = {1558-0520},
abstract = {Human activities have led to climate change, resulting in global warming, ocean warming, and more frequent extreme weather events (EWEs). Each of these has the potential to amplify infectious diseases with skin manifestations. Alterations in the skin microbiome due to rising temperatures and humidity may increase infection risk. Global warming has led to expanding geographic ranges of vector-borne diseases. Warming waters have similarly increased the risk of waterborne diseases. EWEs are associated with increased incidence of cutaneous infections. Land-use change, both a cause and effect of climate change, increases the risk of zoonotic spillover.},
}

@article {pmid41207773,
year = {2026},
author = {Fernandez, K and Mundada, M and So, A and Wei, ML},
title = {Influence of Climate on Atopic Dermatitis.},
journal = {Dermatologic clinics},
volume = {44},
number = {1},
pages = {27-34},
doi = {10.1016/j.det.2025.08.007},
pmid = {41207773},
issn = {1558-0520},
abstract = {Atopic dermatitis (AD) is a chronic, relapsing inflammatory skin disease driven by immune dysregulation and skin barrier defects. This article summarizes the impact of climate change on AD outcomes, focusing on articles published since April 2023. Climate change amplifies environmental stressors, temperature extremes, altered humidity, and rising air pollution, that can trigger or worsen AD symptoms by increasing oxidative stress, disrupting the skin's microbiome, and weakening barrier function. Studies suggest associations between climate variables and AD outcomes, although findings are inconsistent. Strategies such as patient education, indoor air filtration, and broader policy measures to reduce pollution may mitigate climate-related risks.},
}

@article {pmid41207432,
year = {2025},
author = {Afonso, RB and Adivi, LN and Linehan, K and O'Donovan, M and Hill, C and Ross, RP and Stanton, C},
title = {Potential of silage inoculants to mitigate methane production from the rumen: A systematic review.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-27063},
pmid = {41207432},
issn = {1525-3198},
abstract = {Methane (CH4) emissions from enteric fermentation in ruminants represent the largest source of anthropogenic agricultural emissions, contributing significantly to global CH4 levels. Enteric CH4 mitigation strategies have been intensively investigated to address the detrimental effects on climate change and ruminant production characteristics. This systematic review investigated whether microbial silage inoculants could reduce CH4 formation in the rumen microbiome, both ex vivo and in vivo, based on available literature. Two independent reviewers conducted a comprehensive search for peer-reviewed articles, without year restrictions, up to January 31, 2024. The search focused on studies reporting CH4 gas production both in vitro and in vivo. Of 434 articles initially identified, only 10 met the quality criteria and were included in the analysis. Among the selected studies, 9 measured CH4 production using in vitro assays, whereas one reported an in vivo trial. The majority of the experiments (70%) were conducted using cattle rumen samples, including the in vivo study involving cattle, the remainder of the experiments used rumen samples obtained from sheep. Ten bacterial species were used as inoculants across the selected studies. Lactobacillus buchneri, used in combination with additives, achieved the highest CH4 reduction at 83%. Lactobacillus plantarum also showed a significant reduction in CH4 output, achieving a 48% decrease. Overall, 80% of the reviewed studies reported a reduction in CH4 production by ruminant microorganisms following the application of silage microbial inoculants. These findings suggest that silage microbial inoculants hold promise as a strategy to mitigate CH4 emissions in livestock. The limited number of studies highlights the need for further research to confirm these results and explore wider applications.},
}

@article {pmid41207348,
year = {2025},
author = {Wang, X and Liu, P and Yang, L and Zheng, W and Zhu, L and Kong, X},
title = {Integrated analysis of trichlorfon-induced intestinal toxicity in Micropterus salmoides: Barrier Impairment, microbiome disruption, and metabolic reprogramming.},
journal = {Fish & shellfish immunology},
volume = {},
number = {},
pages = {110988},
doi = {10.1016/j.fsi.2025.110988},
pmid = {41207348},
issn = {1095-9947},
abstract = {Trichlorfon is widely used to control parasites but may also induce sublethal effects in fish. However, its chronic effects on intestinal metabolism and toxicity remain unclear. Here, we investigated the effects of chronic trichlorfon exposure (0.01, 0.1, and 1 mg/L) on juvenile largemouth bass through integrated histological, physiological, microbiological, and metabolomic analyses. Trichlorfon exposure disrupted neurotransmitter balance, significantly reducing excitatory neurotransmitters (acetylcholine, glutamate, dopamine) and increasing gamma-aminobutyric acid. Mitochondrial dysfunction induced energetic stress and triggered a metabolic shift from oxidative phosphorylation to anaerobic glycolysis, supported by ATP depletion, accumulation of glycolytic and tricarboxylic acid intermediates, and downregulation of AMPKα1, PGC-1α, SDHa, and SDHb. Oxidative stress caused lipid peroxidation, decreasing linoleic and gamma-linolenic acids, and increasing malondialdehyde. Antioxidant defenses were suppressed, with impaired glutathione metabolism, decreased peroxidase and superoxide dismutase activities. Mucosal barrier was compromised, with disrupted glycosylation precursors, reduced expression of barrier genes (Occludin, ZO-1, Claudin-1), increased of proinflammatory cytokines (IL-1β, IL-6, IL-8, TNF-α), and marked histopathological alterations. Altered polyunsaturated fatty acid metabolism promoted inflammatory eicosanoids (prostaglandin E2, 5(S), 14(R)-lipoxin B4). In addition, digestion and nutrient absorption were impaired, reflected by reduced conjugated bile acids, essential amino acids, and digestive enzyme activities. Gut microbial dysbiosis was observed, with increased opportunistic pathogens and reduced beneficial lactic acid bacteria. Overall, chronic trichlorfon exposure disrupted intestinal homeostasis. This study offers new insights into the intestinal metabolic alterations in fish exposed chronically to trichlorfon and highlights the need for prudent pesticide management in aquaculture.},
}

@article {pmid41207331,
year = {2025},
author = {Carlà, AS and Ianiro, G},
title = {Beneficial effects of physical exercise on anticancer immunity are mediated by gut microbiome metabolites.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2025.11.001},
pmid = {41207331},
issn = {1528-0012},
}

@article {pmid41207298,
year = {2025},
author = {Zhai, Z and Che, X and Shen, W and Zhang, Z and Li, Y and Pan, J},
title = {HLRMDB: a comprehensive database of the human microbiome with metagenomic assembly, taxonomic classification, and functional annotation by analysis of long-read and hybrid sequencing data.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1152},
pmid = {41207298},
issn = {1362-4962},
support = {32470699//National Natural Science Foundation of China/ ; //Chongqing Medical University/ ; },
abstract = {The human microbiome harbours an immense diversity of uncultivated microbes; short-read metagenomic sequencing has elucidated much of this diversity, but fragment repeats and mobile elements constrain strain-level resolution. Fortunately, long-read metagenomic sequencing can generate reads spanning tens of kilobases with single-molecule accuracies exceeding 99%, enabling near-complete genome and gene cluster recovery in a cultivation-independent manner. However, systematic resources that aggregate and standardise long-read outputs remain limited. Here, we present HLRMDB (http://www.inbirg.com/hlrmdb/), a comprehensive database of human microbiome datasets derived from long-read and hybrid metagenomic sequencing. We curated 1672 publicly available metagenomes (1291 long reads; 381 hybrids) spanning 38 studies, 39 sampling contexts and 42 host health states. A uniform assembly and binning pipeline reconstructed >98 Gb of contigs and yielded 18 721 metagenome-assembled genomes (MAGs). These MAGs span 21 phyla and 1323 bacterial species, with 6339 classified as near-complete and 5609 as medium-quality. HLRMDB integrates these genome-resolved data with extensive gene-centric functional profiles and antimicrobial resistance annotations. An interactive web interface supports flexible access to both sample-level and genome-level results, with multiple visualisations linking raw reads to assembled genomes. Overall, HLRMDB offers a harmonised, long-read-oriented repository that supports reproducible, strain-resolved comparative genomics and context-sensitive ecological investigations of the human microbiome.},
}

@article {pmid41207233,
year = {2025},
author = {Basapuram, G and Duttagupta, S and Dutta, A},
title = {Pesticides impact microbial communities in the freshwater ecosystem: Implications on biogeochemical cycles.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140403},
doi = {10.1016/j.jhazmat.2025.140403},
pmid = {41207233},
issn = {1873-3336},
abstract = {Pesticides that discharge from surrounding environments into river water affect the composition and structure of the microbiome, eventually modifying the biogeochemical processes. Microcosm experiments examined the effects of two prevalent pesticides (malathion and atrazine) on the river water microbiome. 16S rRNA gene amplicon sequencing was leveraged to characterize microbiome shifts in the presence and absence of pesticides. Microbial diversity was significantly reduced in the presence of pesticides. The presence of malathion and atrazine in higher abundances promoted the growth of Pseudomonas while inhibiting the expansion of other microorganisms. Principal Coordinates Analysis indicated compelling differences in diversity and metabolic profiles. Shifts in microbial populations involved in carbon, nitrogen, and sulfur cycles were observed in the presence of pesticides. Our findings demonstrated a reduction in microbial populations involved in carbon fixation and sulfur oxidation in samples exposed to pesticides compared to samples unamended with pesticides. With respect to the nitrogen cycle, the microorganisms involved in nitrification and denitrification processes were reduced in the presence of pesticides. This study exemplifies an intricate interplay between pesticide application, microbial diversity, and the associated metabolic activities, which highlights the multifaceted impact of emerging contaminants that contribute to a cascading effect on the biogeochemical cycles.},
}

@article {pmid41207116,
year = {2025},
author = {Obayashi, N and Shintani, T and Morihara, N and Kawada-Matsuo, M and Ando, T and Miyata, R and Hayashi, Y and Kataoka, N and Tanimoto, K and Kawaguchi, H and Komatsuzawa, H and Kajiya, M},
title = {Prevalence and Ecological Role of Streptococcus toyakuensis in Saliva of Healthy Young Individuals.},
journal = {International dental journal},
volume = {76},
number = {1},
pages = {103987},
doi = {10.1016/j.identj.2025.103987},
pmid = {41207116},
issn = {1875-595X},
abstract = {BACKGROUND AND OBJECTIVES: Antimicrobial resistance (AMR) remains a critical global health concern. In 2022, Streptococcus toyakuensis, a newly identified species with potential multidrug resistance, was isolated from the blood of a patient with sepsis. This study aimed to explore the distribution of S. toyakuensis in the oral microbiome of healthy young individuals and to compare the bacterial community composition between the detection and non-detection groups.

METHODS: Sixty saliva samples were randomly collected from 356 healthy young individuals and analyzed using next-generation 16S rRNA sequencing for comprehensive microbial profiling. A taxonomic distribution analysis was performed to compare microbial diversity between S. toyakuensis detection and non-detection groups. Functional analysis identified differentially activated metabolic pathways.

RESULTS: S. toyakuensis was detected in 35 of 60 participants. Beta diversity analysis revealed a significant difference in microbial composition between the groups. Linear discriminant analysis effect size showed higher abundance of Neisseria, Haemophilus, Campylobacter, and Capnocytophaga in the detection group, while Actinomyces predominated in the non-detection group. Functional analysis identified 26 significantly different metabolic pathways, including the glyoxylate cycle and L-methionine biosynthesis superpathway.

CONCLUSION: The high prevalence of S. toyakuensis in the oral microbiome of healthy young individuals highlights the need for further investigation into its role in AMR dissemination.

CLINICAL SIGNIFICANCE: The colonization of S. toyakuensis may influence the oral microbial ecosystem and metabolic activity, potentially facilitating the spread of AMR. Its detection in healthy individuals suggests a silent reservoir, underscoring the importance of oral microbiome surveillance in public health and infection control strategies.},
}

@article {pmid41207099,
year = {2025},
author = {Torres, AHF and Soares, TA and Pereira, RB and Gomes, P and Garrido, SS},
title = {Interplay between the immune system and the microbiome of human skin and its modulation by antimicrobial peptides.},
journal = {International immunopharmacology},
volume = {168},
number = {Pt 1},
pages = {115754},
doi = {10.1016/j.intimp.2025.115754},
pmid = {41207099},
issn = {1878-1705},
abstract = {The cutaneous immune system is essential for protecting the body against pathogens and regulating the skin's immune response, which can be further influenced by the skin's microbiome and also by exogenous bioactive compounds. As such, innovative approaches based on use of antimicrobial peptides and/or probiotics show a promising potential for restoring skin homeostasis and alleviating dermatological conditions. In this connection, herein we revise the immune functions of the skin, covering its structural and cellular components, interactions with the microbiome, and defense mechanisms as well as their modulation by antimicrobial peptides. We further address recent developments in this topic, providing an up-to-date perspective that paves the way for advancing both skin immunology knowledge and new therapeutic interventions for a healthy skin.},
}

@article {pmid41207093,
year = {2025},
author = {Li, Y and Yu, R and Tan, S and Sun, L and Yan, Y and Huang, J and Waseem, MH and Wang, Z and Li, C},
title = {Alterations in the profiles of rumen microbiota and metabolites in Holstein and Jersey dairy cows under heat stress.},
journal = {Journal of thermal biology},
volume = {134},
number = {},
pages = {104327},
doi = {10.1016/j.jtherbio.2025.104327},
pmid = {41207093},
issn = {0306-4565},
abstract = {High temperature impacts the performance and health of dairy cows in summer, causing considerable financial burden in the dairy industry. Differences in physiological changes, rumen microbial diversity and metabolites of Holstein and Jersey dairy cows under heat stress and normal environment were investigated. The present study demonstrates that oxidative stress levels in Holstein and Jersey cows are significantly elevated under conditions of heat stress, while the pro-inflammatory cytokine levels were elevated only in heat-stressed Holstein cows. 16S rDNA gene sequencing showed that heat stress markedly altered the abundance, homogeneity and makeup in the bovine rumen microbiome. Moreover, the significant abundance of Rikenellaceae_RC9_gut_group exhibited a positive association with malondialdehyde (MDA) in Holstein cows, Pseudobutyrivibrio was positively correlated with tumor necrosis factor-α (TNF-α) in the Jersey cows. Metabolomics profiling based on liquid chromatography-mass spectrometry (LC-MS) revealed that totally 1065 metabolites in Holstein cows and 571 metabolites in Jersey cows were significantly changed. The differential metabolites Leucine and Prostaglandin i2 were negatively associated with interleukin (IL)-6, Erucamide was positively related to IL-1β and MDA in Holstein cows. And 9,10-dihydroxy-12z-octadecenoic acid showed a negative correlation with IL-6 and TNF-α in Jersey cows. Besides, the changed rumen microbiome displayed remarkable associations with metabolites. Our results indicated that heat stress caused remarkable alterations of rumen microbiome and metabolism both in Holstein and Jersey dairy cows, the altered ruminal bacteria and metabolic profiles could consecutively affect physiological responses in dairy cows.},
}

@article {pmid41206954,
year = {2025},
author = {Mao, Y and Jiang, Z and Wang, T and Hu, Y and Zhan, X},
title = {TCVS: Tree-guided compositional variable selection analysis of microbiome data.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf617},
pmid = {41206954},
issn = {1367-4811},
abstract = {MOTIVATION: Studies of microbial communities, represented by the relative abundances of taxa at various taxonomic levels, have underscored the significance of microbiota in numerous aspects of human health and disease. A pivotal challenge in microbiome research lies in pinpointing microbial taxa associated with disease outcomes, which could play crucial roles in prevention, detection, and treatment of various health conditions. Alongside these relative abundance data, taxonomic information sometimes offers a unique lens to explore the impact of shared evolutionary histories on patterns of microbial abundance.

RESULTS: In pursuit of this goal, we utilize the tree structure to more flexibly identify taxa associated with disease outcomes. To enhance the accuracy of our selection process, we introduce auxiliary knockoff copies of microbiome features designated as noise. This approach allows for the assessment of false positives in the selection process and aids in refining it towards more precise outcomes. Extensive numerical simulations demonstrate that our methodology outperforms several existing methods in terms of selection accuracy. Furthermore, we demonstrate the practicality of our approach by applying it to a widely used gut microbiome dataset, identifying microbial taxa linked to body mass index.

TCVS R code is available at https://github.com/Yicong1225/TCVS.},
}

@article {pmid41206936,
year = {2025},
author = {Borman, T and Sannikov, A and Finn, RD and Limborg, MT and Rogers, AB and Kale, V and Hanhineva, K and Lahti, L},
title = {HoloFoodR: a statistical programming framework for holo-omics data integration workflows.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf605},
pmid = {41206936},
issn = {1367-4811},
abstract = {SUMMARY: Holo-omics is an emerging research area that integrates multi-omic datasets from the host organism and its microbiome to study their interactions. Recently, curated and openly accessible holo-omic databases have been developed. The HoloFood database, for instance, provides nearly 10,000 holo-omic profiles for salmon and chicken under controlled treatments. However, bridging the gap between holo-omic data resources and algorithmic frameworks remains a challenge. Combining the latest advances in statistical programming with curated holo-omic data sets can facilitate the design of open and reproducible research workflows in the emerging field of holo-omics.

HoloFoodR R/Bioconductor package and the source code are available under the open-source Artistic License 2.0 at the package homepage https://doi.org/10.18129/B9.bioc.HoloFoodR.

SUPPLEMENTARY INFORMATION: Available in the package vignette https://ebi-metagenomics.github.io/HoloFoodR/articles/case_study.html.},
}

@article {pmid41206876,
year = {2025},
author = {Catano, CP and DuBose, JG and Fuller-Hall, L and Chavez, J and de Roode, JC},
title = {Experimental Immigration Mediates Ecological Selection and Drift in Monarch Microbiome Assembly.},
journal = {Ecology letters},
volume = {28},
number = {11},
pages = {e70252},
doi = {10.1111/ele.70252},
pmid = {41206876},
issn = {1461-0248},
support = {IOS-2202255//National Science Foundation/ ; },
abstract = {The distribution of biodiversity depends on processes operating across scales, yet multiscale paradigms have struggled to permeate host-microbiome research. Instead, host-microbiome research has focused on host selection and has struggled to explain the high variation in microbial composition across individuals. By integrating multi-scale ecological theory with experimental manipulation of bacteria colonizing monarch butterfly caterpillars, we test the hypothesis that immigration from the regional species pool alters the importance of niche selection and drift in causing variation in gut bacterial communities across individuals and through ontogeny. Higher immigration increased the dominance of certain bacteria, causing greater convergence in bacterial composition across the caterpillar life stage. Conversely, limited immigration made colonization more stochastic, resulting in more unpredictable variability in bacterial composition across individuals. Our study reveals that immigration mediates the balance between host selection and drift, demonstrating that processes operating at scales beyond the individual are underappreciated but critical for structuring host-microbiome symbioses.},
}

@article {pmid41206864,
year = {2025},
author = {Docherty, JAD and Cook, R and Kiu, R and Dyball, X and Brown, TL and Kujawska, M and Smith, RL and Phillips, S and Watt, R and Telatin, A and Tiwari, SK and Hall, LJ and Adriaenssens, EM},
title = {Diverse defense systems and prophages in human-associated Bifidobacterium species reveal coevolutionary "arms race" dynamics.},
journal = {Cell reports},
volume = {44},
number = {11},
pages = {116542},
doi = {10.1016/j.celrep.2025.116542},
pmid = {41206864},
issn = {2211-1247},
abstract = {Bacteria of the genus Bifidobacterium are pivotal for human health, especially in early life, where they dominate the gut microbiome in healthy infants. Bacteriophages, as drivers of gut bacterial composition, can affect bifidobacterial abundance. Here, we use a bioinformatics approach to explore direct interactions between human-associated Bifidobacterium spp. and prophages, as evidenced by their genomes. Analysis of 1,086 bifidobacterial genomes reveals the presence of complex systems that prevent viral invasion, with 34 defense systems and 56 subtypes detected, including several different CRISPR-Cas systems. CRISPR spacers target almost three-quarters of bifidobacteria-derived prophages, indicating dynamic interactions. At least one prophage is present in ∼67% of strains, with phages exhibiting high genomic diversity and evidence of historical recombination. These prophages encode various defense and anti-defense systems, such as anti-CRISPR genes and restriction-modification mechanisms. Overall, this investigation reveals that coevolutionary "arms race" dynamics drive genomic diversity in both bifidobacteria and their phages.},
}

@article {pmid41206708,
year = {2025},
author = {Royer, FP and Schlick-Steiner, JS and Klammsteiner, T and Kopf, T and Schlick-Steiner, BC and Steiner, FM},
title = {Bacterial communities of wild bee species and the western honey bee (Apis mellifera) (Hymenoptera: Apoidea): Alpine insights.},
journal = {Journal of insect science (Online)},
volume = {25},
number = {6},
pages = {},
doi = {10.1093/jisesa/ieaf095},
pmid = {41206708},
issn = {1536-2442},
abstract = {Wild bees are decreasing in species diversity and populations due to human impact. The abundance of the western honey bee (Apis mellifera L.) experiences an inverse trend, enhancing competition with wild bees and the probability of microbiome exchange. Addressing this exchange, we studied the gut microbiome composition of wild and honey bees, focusing on patterns indicating honey bee influence. Three solitary wild bee species (large scabious mining bee [Andrena hattorfiana F.], grey-backed mining bee (Andrena vaga Panzer), and European orchard bee [Osmia cornuta Latreille]) as well as bumble bees as representatives of eusocial wild bees (Bombus spp. Latreille) and honey bees were sampled in the Austrian Alps. Subsequent 16S ribosomal DNA sequencing revealed the composition of the bacterial communities. The bee groups differed concerning their bacterial composition, with honey bees having the least variation among individuals and a low number of exclusive bacterial taxa and bumble bees the highest bacterial diversity. High honey bee densities corresponded with lower bacterial diversity in wild bees and a higher bacterial similarity between wild and honey bees. Some bacterial taxa were found for the first time in the studied bee groups. Furthermore, the composition of bacterial communities differed between solitary and social bees. We found the first hints that high honey bee density negatively impacts wild bees through alterations of wild bee microbiomes. Future studies should focus on understanding microbiome transmission mechanisms and their consequences for wild bees. Suggestions on how to consider wild bee fitness are indispensable in halting the biodiversity crisis.},
}

@article {pmid41206461,
year = {2025},
author = {Kifushi, M and Nishikawa, Y and Hosokawa, M and Anai, T and Takeyama, H},
title = {Strain-level dissection of complex rhizoplane and soil bacterial communities using single-cell genomics and metagenomics.},
journal = {DNA research : an international journal for rapid publication of reports on genes and genomes},
volume = {},
number = {},
pages = {},
doi = {10.1093/dnares/dsaf032},
pmid = {41206461},
issn = {1756-1663},
abstract = {Root exudates shape root-associated microbial communities that differ from those in soil. Notably, specific microorganisms colonize the root surface (rhizoplane) and strongly associate with plants. Although retrieving microbial genomes from soil and root-associated environments remains challenging, single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) are essential for studying these microbiomes. This study compared SAGs and MAGs constructed from short-read metagenomes of the same soil samples to clarify their advantages and limitations in soil and root-associated microbiomes, and to deepen insights into microbial dynamics in rhizoplane. We demonstrated that SAGs are better suited than MAGs for expanding the microbial tree of life in soil and rhizoplane environments, due to their greater gene content, broader taxonomic coverage, and higher sequence resolution of quality genomes. Metagenomic analysis provided sufficient coverage in the rhizoplane but was limited in soil. Additionally, integrating SAGs with metagenomic reads enabled strain-level analysis of microbial dynamics in the rhizoplane. Furthermore, SAGs provided insights into plasmid-host associations and dynamics, which MAGs failed to capture. Our study highlights the effectiveness of single-cell genomics in expanding microbial genome catalogs in soil and rhizosphere environments. Integrating high-resolution SAGs with comprehensive rhizoplane metagenomes offers a robust approach to elucidating microbial dynamics around plant roots.},
}

@article {pmid41206083,
year = {2025},
author = {Jain, SG and Vennam, SS and Dharmatti, G and Huey, SL and Kaur, P and Krishnan, S and Nandi, BK and Puri, S and Sesikaran, B and Srinivasan, S and Udipi, S and Voruganti, VS},
title = {Principles and Guidelines for the Practice of Precision Nutrition in the Indian Context: A Narrative Review.},
journal = {Nutrition reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/nutrit/nuaf177},
pmid = {41206083},
issn = {1753-4887},
support = {//International Life Sciences Institute India (ILSI INDIA)/ ; },
abstract = {Precision and personalized nutrition represent a transformative shift in dietary recommendations, moving away from a one-size-fits-all approach to a more individualized strategy that considers genetics, epigenetics, the microbiota, and socio-cultural, environmental, and lifestyle factors. As the field of precision medicine evolves, clear principles and guidelines are essential for its application in clinical and public health settings. In this narrative review we aimed to provide the current principles and guidelines governing personalized nutrition to establish a comprehensive and standardized framework for effective application and development of personalized nutrition strategies. In this review we also emphasized the importance of involving regional and cultural perspectives while formulating nutritional plans with a particular focus on individuals with an Indian background. A comprehensive search of key databases spanning the past two decades identified several core principles of precision nutrition and their integration with sociocultural factors. The guidelines emphasize interdisciplinary approaches and technological advancements like AI and big data and also point toward the applicability and generalizability of these approaches across cultures and populations, specifically Indian. However, the integration of multiple data sources and the requirement for uniform protocols are major challenges. Notwithstanding these challenges, the field of individualized nutrition has great promise for the future of nutrition. Future research should focus on refining these guidelines and addressing existing gaps to enhance their efficacy and applicability in real-world settings.},
}

@article {pmid41206012,
year = {2025},
author = {Tan, EK and Wang, JDJ and Pettersson, S and Wang, Q and Takahashi, R and Poewe, W and Jankovic, J and Rascol, O},
title = {Faecal microbiota transplant for Parkinson's disease: promises and future directions.},
journal = {Brain : a journal of neurology},
volume = {},
number = {},
pages = {},
doi = {10.1093/brain/awaf419},
pmid = {41206012},
issn = {1460-2156},
abstract = {There is considerable evidence linking alterations in gut microbiome composition with Parkinson's disease (PD), leading to several recent randomized controlled fecal microbiota transplantation (FMT) trials in PD patients targeting gut dysbiosis with the aim to modulate the gut-brain axis. Some FMT trials have observed motor and non-motor symptoms improvements in PD patients, possibly through microbiota linked enhanced short-chain fatty acid or other metabolite effects and reduced systemic inflammation. While the findings are exciting and can potentially open a new treatment paradigm, crital questions on donor selection, the optimal screening and selection of the donor microbiome, delivery routes and the timing and frequency of transplantation need to be addressed. We suggest that future FMT trials should incorporate blood, metabolites, urine and functional neuroimaging biological markers and control dietary, lifestyle comorbidities, medication intake and/or other potential variables, and to ensure optimal evaluation of interactions between the gut microbes and brain outcomes prospectively over a longer time frame.},
}

@article {pmid41205933,
year = {2025},
author = {Favaron, A and Sangfuang, N and McCoubrey, LE and Awad, A and Ghyselinck, J and Marzorati, M and Verstrepen, L and De Munck, J and De Medts, J and Basit, AW and Orlu, M},
title = {Assessing the effects of tofacitinib on the gut microbiome in inflammatory bowel disease.},
journal = {European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences},
volume = {},
number = {},
pages = {107365},
doi = {10.1016/j.ejps.2025.107365},
pmid = {41205933},
issn = {1879-0720},
abstract = {Gut microbiota dysbiosis and impaired epithelial barrier function play a key role in inflammatory bowel disease (IBD). Tofacitinib citrate, a Janus kinase (JAK) inhibitor approved for IBD, modulates immune responses via the JAK-STAT (Janus kinase-signal transducer and activator of transcription) pathway, yet its effects on the gut microbiome remain unclear. Here, we employed the short-term colon model (ProDigest, BE) containing human microbiota from three Crohn's Disease donors to assess fermentative and metabolic activities and microbial composition following 48 h of tofacitinib treatment. A Caco-2/THP1 co-culture system was used to assess the impact of tofacitinib on epithelial immunomodulation and barrier integrity. Tofacitinib did not significantly affect microbiota composition and fermentative or metabolic activity. However, it consistently reduced pro-inflammatory chemokines motif chemokine ligand 10 (CXCL10) and monocyte chemoattractant protein-1 (MCP-1), and interleukin-6 (IL-6) in specific donors, indicating targeted immunomodulatory effects. These findings suggest that while tofacitinib may have a minimal impact on microbiota function, it may exert anti-inflammatory effects via microbiota-derived metabolites. The short-term colon model represents a robust platform for investigating microbiome-drug interactions relevant to IBD.},
}

@article {pmid41205808,
year = {2025},
author = {Cohen, S and Donovan, M and Gardner, D and Sambo, D and Karagoz, SB and Cinar, R and Goldman, D and Gardner, JD and Pacher, P and Paloczi, J},
title = {Selective Depletion of Gut Gram-Negative Bacteria Attenuates Alcohol-Binge-Induced Cardiovascular Dysfunction by Lowering Cardiac Anandamide Levels.},
journal = {The American journal of pathology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajpath.2025.10.010},
pmid = {41205808},
issn = {1525-2191},
abstract = {Binge drinking contributes to a rising number of emergency room visits in the United States. Our previous work demonstrated that an alcohol binge impairs cardiac performance and exerts complex hemodynamic effects through the activation of the endocannabinoid-mediated cannabinoid receptor 1 (CB1R) signaling pathway. Anandamide (AEA), an endogenous CB1R agonist, is synthesized in response to various stressors and tissue injury. However, the role of binge drinking in increasing myocardial AEA levels, which leads to CB1R-dependent cardiodepression, remains unclear. Here, we studied how endotoxins from intestinal Gram-negative bacteria affect myocardial AEA levels, which further induce CB1R-dependent cardiac dysfunction following acute alcohol intoxication. Using a murine model of a single alcohol binge (5 g/kg orally), we observed reduced mesenteric microcirculation concurrent with elevated circulating endotoxin levels. Selective depletion of gut Gram-negative bacteria by antibiotics partially ameliorated alcohol-induced gut barrier dysfunction, significantly lowered circulating endotoxins, coinciding with reduced cardiac AEA levels at 3 hours post-binge. These changes were paralleled with moderately improved cardiac performance, and vascular tone. Cardiac RNA levels of genes involved in AEA synthesis increased after alcohol binge, but not in antibiotic-pretreated mice. However, acute alcohol-induced cardiac AEA formation was unrelated to Toll-like receptor-4 signaling. These findings provide novel insights that highlight the pivotal role of intestinal Gram-negative bacteria in modulating cardiac AEA levels after an alcohol binge, leading to cardiovascular dysfunction.},
}

@article {pmid41205786,
year = {2025},
author = {Weltz, TK and Peng, S and Larsen, A and Bak, EEF and Tran, JVQ and Hemmingsen, MN and Ørholt, M and Mielke, LV and Trillingsgaard, J and Elberg, JJ and Hölmich, LR and Jensen, LT and Vester-Glowinski, P and Fritz, B and Bjarnsholt, T and Trivedi, U and Li, X and Sørensen, SJ and Herly, M},
title = {Breast Implant microbiome profile correlates with foreign body response severity.},
journal = {Acta biomaterialia},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.actbio.2025.11.008},
pmid = {41205786},
issn = {1878-7568},
abstract = {Biomedical implants significantly enhance quality of life for millions of individuals worldwide. However, maintaining long-term implant function remains challenging, and it is often due to a severe foreign body response, characterized by fibrosis and functional impairment, clinically referred to as capsular contracture for breast implants. Colonization of implant surfaces by low-virulent bacteria has been proposed as a potential driver of severe foreign body response, but evidence from large-scale human studies has been lacking. We found that the implant microbiome composition is significantly associated with the foreign body response severity based on an extensive characterization of the breast implant microbiome using 16S rRNA gene amplicon sequencing. We analyzed 339 explanted breast implants from 206 patients undergoing revisional surgery without any symptoms of a clinical infection. We detected a diverse community of bacteria on the implants and demonstrated that an increased relative abundance of Staphylococcus was associated with a severe foreign body response. This pattern was supported by a within-patient analysis of 20 individuals with unilateral severe versus contralateral mild foreign body response. These findings suggest that the implant microbiome plays a role in the development of a severe foreign body response and may guide strategies to improve implant biocompatibility. STATEMENT OF SIGNIFICANCE: : This study identified a diverse microbiome on breast implants from patients without any symptoms of infection and demonstrated a clear association between microbiome composition and the severity of the foreign body response (FBR), a significant complication affecting implant function. Notably, implants with severe FBR showed lower microbial diversity and higher relative abundance of Staphylococcus compared to those with mild FBR. Additionally, a paired analysis within patients with severe FBR in one breast and mild FBR in the contralateral breast further supported higher relative Staphylococcus abundance on the severe FBR implant. These findings provide insights into microbial factors influencing implant biocompatibility, which may guide strategies to improve implant biocompatibility and reduce complications for patients.},
}

@article {pmid41205726,
year = {2025},
author = {Tao, H and Mao, K and Zhang, Z and Wei, W and Huang, X and Chen, Y and Mei, S and Tian, X},
title = {Applications of traditional Chinese medicine in cancer immunotherapy via gut microbiota modulation: Current status, mechanisms, challenges and perspectives.},
journal = {Pharmacological research},
volume = {},
number = {},
pages = {108020},
doi = {10.1016/j.phrs.2025.108020},
pmid = {41205726},
issn = {1096-1186},
abstract = {Cancer immunotherapy faces significant limitations due to therapeutic resistance. Emerging evidences have identified the gut microbiota (GM) as a crucial regulator of antitumor immunity through its effects on the tumor immune microenvironment (TIME). Guided by the principle of "fu zheng qu xie" (fortifying healthy qi to reinforce immune homeostasis and eliminating pathogenic factors to promote immune clearance), traditional Chinese medicine (TCM) exerts multi-target systemic regulation. Specifically, TCM modulates gut microecology, which in turn regulates the production of microbial metabolites (e.g., short-chain fatty acids, bile acids), ultimately reprogramming TIME by enhancing immune cell infiltration into the tumor parenchyma, optimizing T-cell cytotoxicity and differentiation, improving antigen presentation, and alleviating immunosuppression. This review systematically summarizes the causal chain of "TCMGMmetabolitesimmune cellsTIME" across different immune phenotypes, emphasizing how bioactive TCM components and classical formulas reshape microbial communities, enrich beneficial bacteria, and regulate metabolic pathways to potentiate cancer immunotherapy. Despite promising preclinical data, challenges persist due to mechanistic complexity, the lack of standardization, and limited clinical translation. Potential solutions include multi-omics integration, intelligent screening of herbal compounds, and targeted delivery systems. With advancing pharmacological insights, TCM-derived microbiome modulators (TMMs), defined as phytochemicals and formulations that systematically modulate gut microecology, may overcome immunotherapy resistance, representing a novel strategy for enhancing cancer immunotherapy.},
}

@article {pmid41205590,
year = {2025},
author = {Golob, JL and Oskotsky, TT and Tang, AS and Roldan, A and Chung, V and Ha, CWY and Wong, RJ and Flynn, KJ and Chai, R and Dubin, C and Parraga-Leo, A and Wibrand, C and Minot, SS and Oskotsky, B and Andreoletti, G and Kosti, I and Bletz, J and Nelson, A and Gao, J and Wei, Z and Chen, G and Tang, ZZ and Novielli, P and Romano, D and Pantaleo, E and Amoroso, N and Monaco, A and Vacca, M and De Angelis, M and Bellotti, R and Tangaro, S and Wang, Z and Yao, J and Goel, A and Mao, J and Wang, H and Zhang, Y and Tewari, A and Kuntzleman, A and Bigcraft, I and Techtmann, S and Bae, D and Kim, E and Jeon, J and Joe, S and , and Theis, KR and Ng, S and Lee, YS and Diaz-Gimeno, P and Bennett, PR and MacIntyre, DA and Stolovitzky, G and Lynch, SV and Albrecht, J and Gomez-Lopez, N and Romero, R and Stevenson, DK and Aghaeepour, N and Tarca, AL and Costello, JC and Sirota, M},
title = {Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102428},
doi = {10.1016/j.xcrm.2025.102428},
pmid = {41205590},
issn = {2666-3791},
}

@article {pmid41205569,
year = {2025},
author = {Mayr, AV and Weinhold, A and Nolzen, A and Keller, A and Ayasse, M},
title = {The neonicotinoid Acetamiprid alters the chemical profile of the primitive eusocial bee Lasioglossum malachurum.},
journal = {Ecotoxicology and environmental safety},
volume = {306},
number = {},
pages = {119311},
doi = {10.1016/j.ecoenv.2025.119311},
pmid = {41205569},
issn = {1090-2414},
abstract = {The widespread use of agrochemicals, particularly neonicotinoids, poses a significant threat to the health of (pollinating) insects. Various health traits are affected, but the impact on the chemical communication of wild bees remains a poorly studied aspect. Here, we assessed how field-realistic exposure to the 'honeybee-safe' neonicotinoid Acetamiprid affects the behaviour, cuticular lipids and microbiome of Lasioglossum malachurum, a small ground-nesting sweat bee. L. malachurum is an important, abundant pollinator of several crop plants with primitive social behaviour which relies on cuticular lipids for communication. We collected bees in the field for a controlled pesticide treatment in the lab. Pesticide-treated individuals increased their sugar-water consumption rate compared to the control group. After 7 days of experiment, the treatment group showed a trend towards less developed ovaries and an increased amount of odour with significantly altered queen pheromones. While the microbiome was not affected by the treatment, a comparison with field individuals showed an erosion of their gut microbiome with a reduction in Apilactobacillus during laboratory keeping. Our findings indicate that neonicotinoids may disturb chemical communication in L. malachurum and thus might impair social behaviour. This raises concerns about the threats of currently approved pesticides to wild pollinators.},
}

@article {pmid41205563,
year = {2025},
author = {Bautzmann, R and Waelchli, J and Schürch, S and Schlaeppi, K and Rentsch, D},
title = {Biodegradable plastics impair maize growth and reshape bacterial communities associated with roots and sand or soil.},
journal = {Ecotoxicology and environmental safety},
volume = {306},
number = {},
pages = {119353},
doi = {10.1016/j.ecoenv.2025.119353},
pmid = {41205563},
issn = {1090-2414},
abstract = {Biodegradable plastics entering terrestrial ecosystems raise environmental and food safety concerns, as they impact soil-plant systems either directly by releasing compounds during degradation, or indirectly, by altering soil biophysical properties and/or microbial communities. Here, we examined the impact of biodegradable micro- and macroplastics made from Mater-Bi, and starch (a simple carbon [C] source present in the plastic studied) on the growth of Zea mays seedlings and bacterial communities associated with roots or with the growth substrates, i.e., sand or silt loam soil. Increasing concentrations of biodegradable plastics and starch reduced plant biomass and chlorophyll content in a dose-dependent manner. Additionally, nitrogen (N) content was reduced, accompanied by lower transcript levels of genes commonly downregulated under N-limiting conditions. Biodegradable plastics and starch altered the bacterial community composition, resulting in decreased bacterial diversity in the growth substrates and increased diversity within maize roots. The effects on maize and bacteria were consistent but generally stronger in sand than in silt loam soil. A follow-up experiment confirmed that plastics- or starch-associated microbes did not affect maize growth when no plastics or starch was present. Our results suggest that biodegradable plastics significantly impair soil-plant systems through their C inputs.},
}

@article {pmid41205502,
year = {2025},
author = {Song, HW and An, J and Sha, JQ and Hu, FY and Liu, WT},
title = {Ca(II) alleviates microplastic toxicity to Microcystis aeruginosa via cyanobacteria induced carbonate precipitation.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140341},
doi = {10.1016/j.jhazmat.2025.140341},
pmid = {41205502},
issn = {1873-3336},
abstract = {Microplastics (MPs), as a globally emerging contaminant, present significant and increasing threats to aquatic ecosystem health and adversely impact cyanobacterial physiology. Ca(II) are ubiquitous essential ions in natural waters, yet their influence on MPs toxicity to cyanobacteria remains insufficiently understood. This study systematically investigated the mitigating effects and mechanisms of Ca(II) on MPs-induced toxicity in Microcystis aeruginosa through an integrated approach involving toxicological assays, microscopic characterization, and microbiome analysis. Both low (2 mg L[-1]) and high (10 mg L[-1]) concentrations of MPs induce oxidative stress and inhibit the growth of M. aeruginosa. However, the addition of Ca(II) significantly mitigated these adverse effects. Mechanistically, Ca(II) promoted cyanobacteria induced carbonate precipitation (CICP), leading to the immobilization of approximately 32.3-34.7 % of MPs, thereby reducing cellular exposure to MPs. Consequently, this attenuated MPs-induced stress on glucosiolate biosynthesis and 2-oxocarboxylic acid metabolism pathways, while mitigating damage to photosynthetic components, including photosystem II (PSII), photosystem I (PSI), and the photosynthetic electron transport chain (PETC). This study provides evidence that Ca(II) protects M. aeruginosa from MPs toxicity by activating the CICP pathway to establish a calcite-based defense system. These findings enhance our understanding of cyanobacteria-MPs interactions under environmentally relevant ionic conditions.},
}

@article {pmid41205302,
year = {2025},
author = {Camille, E and Sébastien, B and Virginie, B},
title = {The hidden players: The mycobiome of pancreatic ductal adenocarcinoma tumors.},
journal = {Microbiological research},
volume = {303},
number = {},
pages = {128392},
doi = {10.1016/j.micres.2025.128392},
pmid = {41205302},
issn = {1618-0623},
abstract = {The microorganisms that inhabit the human body are known to play a role in human health and disease. Continuing to elucidate their specific role in disease progression is, however, necessary. The imbalance of these microorganisms-known as dysbiosis-has been linked to a myriad of intestinal diseases, and more recently to cancer. Despite making up less than 0.1 % of the human microbiome, dysbiosis of the fungal component of the microbiome-the mycobiome-has been found to contribute to the tumorigenesis and progression of certain types of tumors, pancreatic ductal adenocarcinoma (PDAC) included. The quantity and composition of the mycobiome was found to differ between healthy pancreatic tissue, the gut mycobiome of PDAC patients and PDAC tissue. Moreover, in a murine model of PDAC, it was shown that fungal ablation had a protective effect on tumor growth, and that specific fungal species, such as Malassezia globosa, contribute to tumor growth as well as to the inflammatory environment observed in PDAC tumors which promotes tumor progression. Research shows that fungal presence contributes to shaping the immune microenvironment through the activation of the complement system and/or by eliciting a type 2 immune response. Despite these preliminary findings, given the novelty of the field and of the bioinformatics pipelines used to analyze sequencing data, standardized approaches are still under development, thus leading to disagreement on the reliability of these results. The purpose of this review is to provide an up-to-date overview of the current research regarding the contribution of the fungal mycobiome in PDAC tumor progression and the overall tumor microenvironment (TME) of PDAC tumors.},
}

@article {pmid41205272,
year = {2025},
author = {Ai, Y and Davis, AB and Basta, NT and Lee, J},
title = {Unveiling profiles: Dredged materials from Lake Erie harbors are reservoirs for toxic cyanobacteria, antimicrobial resistance, and nutrients.},
journal = {The Science of the total environment},
volume = {1005},
number = {},
pages = {180879},
doi = {10.1016/j.scitotenv.2025.180879},
pmid = {41205272},
issn = {1879-1026},
abstract = {The beneficial use of dredged materials (DMs) as an agricultural resource has gained popularity. Lake Erie shorelines are the most dredged of the Great Lakes in the United States, which is also affected by anthropogenic-driven harmful algal blooms (HAB) and other pollutants like antibiotic resistance genes (ARGs). This study focused on characterizing the DMs from six harbors along the southwest shore of Lake Erie, focusing on the toxic cyanobacteria, toxins, nutrients, microbiome, resistome, and their bacterial hosts. Dominated toxic cyanobacteria genera in DMs are Microcystis, Dolichospermum, Nostoc, Aphanizomenon, and Planktothrix. with microcystin (MC)-producing Microcystis being the major toxin producer. In line with the spatial bloom distribution in Lake Erie, from the central to western basin, the concentration of MC and toxic cyanobacteria in DMs increased. The same spatial trend was observed regarding the ARG, nitrogen, and phosphorus concentrations in DMs. The concentration of clinically relevant ARGs (blaKPC, blaNDM, blaOXA-48, tetQ, and sul1) was positively correlated with the toxic cyanobacteria, N, and P concentrations. Overall, this study provides valuable information on DMs from cyanobacteria- and AR-affected eutrophicated lakes, so safe DM management plan and dredging operations can be possible to sustain beneficial use of DMs in the HAB-affected areas.},
}

@article {pmid41205133,
year = {2025},
author = {Ghafoor, DD and Ahmad, DO and Najmuldeen, HH and Mohammed, SJ and Jalal, PJ and Mustafa, FS and Alghofaili, F and Zangana, BA and Al-Bajalan, SJ},
title = {Multiple sclerosis pathophysiology: a comprehensive review of genetic, environmental, and immunological drivers.},
journal = {Inflammopharmacology},
volume = {},
number = {},
pages = {},
pmid = {41205133},
issn = {1568-5608},
abstract = {Multiple sclerosis (MS) is a complex, chronic neuroinflammatory and neurodegenerative disorder of the central nervous system. This comprehensive review synthesizes evidence to argue that the paramount challenge in MS is bridging the disconnect between anti-inflammatory therapies and ineffective neuroprotective strategies, necessitating a dual-target approach. The paper discusses the crucial roles of genetic predisposition, highlighting the HLA-DRB1*15:01 allele and other non-HLA loci, and environmental triggers, such as Epstein-Barr virus infection, vitamin D deficiency, and smoking. We detail the dysregulation of both T-cells (Th1 and Th17 subsets) and B-cells in the autoimmune attack on myelin, as well as the intricate mechanisms of neurodegeneration, axonal damage, and the challenges of remyelination. The review also incorporates emerging insights into the role of the gut microbiome and epigenetic modifications, underscoring the necessity of an integrative model to understand MS pathogenesis. Ultimately, this review provides a foundational understanding of converging biological drivers of MS. Therapeutically, currently approved disease-modifying therapies (DMTs)-including interferon-β, glatiramer acetate, oral S1P modulators, fumarates, teriflunomide, cladribine, natalizumab, and anti-CD20 monoclonals-reduce relapse frequency and MRI activity but do not eliminate disability progression, particularly in progressive MS. Acute relapses are treated with high-dose corticosteroids, with plasma exchange reserved for steroid-refractory cases. We therefore argue that future success requires integrated strategies that couple sustained control of peripheral inflammation with CNS-intrinsic neuroprotection and remyelination. Therapeutically, modern disease-modifying therapies (interferon-β, glatiramer acetate, oral S1P modulators, fumarates, teriflunomide, cladribine, natalizumab, anti-CD20 monoclonals including ocrelizumab, ofatumumab, and ublituximab) reduce relapse rates and MRI activity yet do not consistently prevent disability progression-particularly in non-active progressive MS. Acute relapses are treated with high-dose corticosteroids; plasma exchange is reserved for steroid-refractory attacks. These realities motivate mechanism-informed strategies that pair sustained immune control with CNS-intrinsic neuroprotection and remyelination.},
}

@article {pmid41205097,
year = {2025},
author = {Lee, SJ and Lee, YS and Kim, YR and Jeon, MH and Noh, DI and Jeong, SM and Kim, KW and Lee, EW and Jang, WJ},
title = {Development of Novel Host-Associated Low-Temperature Probiotics (HALP) Tailored to Aquaculture Applications.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41205097},
issn = {1867-1314},
support = {R2025038//National Institute of Fisheries Science/ ; 2022R1A2C1012655//National Research Foundation of Korea/ ; RS-2024-00403688//Korea Basic Science Institute/ ; },
abstract = {Aquaculture temperatures vary depending on the fish species, and probiotics used in aquaculture must remain effective under these conditions. Therefore, our study developed host-associated low-temperature probiotics (HALP) adapted to temperature conditions relevant to aquaculture. Three bacterial strains, Rahnella inusitata NBL2302 (RI), Pseudoalteromonas arctica NBL2303 (PA), and Lactiplantibacillus plantarum NBL2306 (LP), were isolated from the gastrointestinal tract of Korean rockfish (Sebastes schlegelii). Safety assessments, in vitro probiotic characterization (including antioxidant activity, acid/salt/bile tolerance, antimicrobial activity, and adhesion), and a feeding trial were conducted. All three strains were confirmed to be safe, exhibiting no hemolytic or cytotoxic activity. Among the three strains, LP exhibited the highest adhesion to intestinal epithelial cells and showed antimicrobial activity against fish pathogens. RI supplementation significantly enhanced innate immune markers such as serum total protein (TP), triglycerides (TG), and myeloperoxidase (MPO), along with the upregulation of immune-related genes (HSP70, IL-1β, TNF-α) (p < 0.05). PA supplementation resulted in the greatest weight gain and significantly improved specific growth rate (SGR), likely due to increased digestive enzyme activity. LP promoted immunostimulatory responses (elevated expression of MPO, TP, HSP70, and TNF-α) and pronounced changes in the beta diversity of the gut microbiota. Microbiome analysis revealed that LP-fed fish harbored higher abundances of beneficial genera such as Pseudomonas, Ralstonia, and Sphingomonas. Overall, each strain displayed unique characteristics and exerted distinct effects during feeding trials. These findings, which take host temperature preferences into account, underscore the potential of HALP in aquaculture and highlight the need for further research into optimized combination strategies.},
}

@article {pmid41204383,
year = {2025},
author = {Issifu, S and Elango, AV and Michl, K and David, C and Cernava, T and Wilhelm, RC and Rasche, F},
title = {Perennial Kernza cropping promotes rhizosphere microbiome stability and endophyte recruitment compared to annual wheat.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {139},
pmid = {41204383},
issn = {2524-6372},
support = {RA 1717/8-1//Deutsche Forschungsgemeinschaft/ ; },
abstract = {BACKGROUND: Perennial cropping systems are increasingly recognized for their potential to enhance microbial biodiversity and beneficial soil functions compared to annual crops. The impact of perennialization on the rhizomicrobiome and endophyte community was assessed by comparing intermediate wheatgrass (Thinopyrum intermedium, commercialized as Kernza®, hereafter called 'Kernza') and annual wheat (Triticum aestivum) associated communities across a north-south European agroclimatic gradient (Sweden, Belgium, and France) over two growing seasons and at two depths.

RESULTS: Between the 2 years, the Kernza-associated rhizomicrobiome was more stable and exhibited greater homogeneity across depths compared to annual wheat. Kernza harboured a significantly more diverse set of crop-associated amplicon sequence variants (ASVs) and had a higher number of core ASVs than annual wheat. Furthermore, Kernza had a significantly higher proportion of rhizobacterial populations in root tissues than annual wheat. Environment-wide association analyses revealed that the Kernza rhizosphere had higher proportions of grassland-associated and rhizosphere-dwelling microbiomes compared to annual wheat. Despite these noteworthy differences, the greatest variation in the rhizomicrobiome composition was driven by factors such as country, year, and depth, rather than crop type. For instance, Actinobacteriota dominated rhizobacterial communities in both Kernza and annual wheat.

CONCLUSIONS: Overall, Kernza conferred modest yet clear improvements in rhizomicrobiome community stability and selective endophyte recruitment, supporting its ability to enhance sustainable, microbially-mediated soil functions. Moreover, Kernza hosted significant grassland-associated taxa, suggesting a similarity between Kernza fields and grassland ecosystems.},
}

@article {pmid41204381,
year = {2025},
author = {Villette, R and Sunyer, JO and Novikova, PV and Aho, VTE and Petrov, VA and Hickl, O and Busi, SB and De Rudder, C and Kunath, BJ and Heintz-Buschart, A and Trezzi, JP and Halder, R and Jäger, C and Lebrun, LA and Daujeumont, A and Schade, S and Janzen, A and Jehmlich, N and von Bergen, M and Laczny, CC and May, P and Trenkwalder, C and Oertel, W and Mollenhauer, B and Wilmes, P},
title = {Correction: Integrated multi‑omics highlights alterations of gut microbiome functions in prodromal and idiopathic Parkinson's disease.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {230},
pmid = {41204381},
issn = {2049-2618},
}

@article {pmid41204312,
year = {2025},
author = {Sun, W and Liu, Q and Chen, H and Xie, X and Zhang, Z and Zeng, Y and Zhou, J and Zhou, X and Jiang, X and Liang, Z and Li, JF and Deng, Y},
title = {Rice phyllospheric Pantoea spp. suppress blast and bacterial blight diseases.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {137},
pmid = {41204312},
issn = {2524-6372},
support = {2022YFA1304402; 2023YFD1400200//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Rice is a major food crop in China as well as Asia, yet its production is threatened by microbial diseases including blast disease caused by fungal pathogen (Magnaporthe oryzae) and bacterial blight caused by several bacterial pathogens. To screen for bacterial microbiota associated with rice blast occurrence, and/or contributing to disease resistance, we performed microbiota analysis with rhizosphere soil, root, stem, and leaf samples of blast susceptible (CO39) and resistant (Y33R) rice grown in a blast disease nursery garden.

RESULTS: Our result showed no significant difference in microbiota of rhizosphere soil, root, or leaf between these two rice cultivars, but stem microbiota were significantly different. Pantoea spp. were enriched in stem of blast susceptible rice, suggesting that it may play a role after fungal infection. A total of 822 bacterial strains were isolated from the phyllospheric (including leaf and stem) samples of Y33R and CO39 rice. Based on 16S rRNA amplicon sequencing, and phylogenic analysis using 16S rRNA, gyrB, leuS, and rpoB gene sequences, the 3 isolated strains and 1 strain were identified as P. ananatis and P. dispersa, respectively. The strains A25-H1 and B10-A1 were selected for genome sequencing, and based on Average Nucleotide Identity (ANI) analysis, we confirmed that A25-H1 was P. ananatis and B10-A1 was P. dispersa. The P. ananatis consortium (A25-F1, A25-G1, and A25-H1 combination) A25-11 and P. dispersa strain B10-A1 displayed suppressive effect on blast disease when they were applied to the susceptible rice CO39. Although a P. ananatis strain SC7 has been reported to cause bacterial blight in rice, A25-11 or B10-A1 was non-pathogenic to rice under experimental conditions. Furthermore, they could also suppress bacterial blight caused by SC7 or Xanthomonas oryzae pv. oryzae strain Pxo99A. A25-11 and B10-A1 did not affect the growth of M. oryzae mycelia in confrontation culture analysis, but induced transcription of rice immunity genes and promoted ROS accumulation, suggesting that the biocontrol effect of A25-11 or B10-A1 may lie on immunity priming. We further showed that A25-11 and B10-A1 possessed growth promoting capacity including indole 3-acetic acid (IAA) production, phosphate solubilization, nitrogen fixation, and siderophore production. Under field condition, the consortium A25-11 and strain B10-A1 could effectively suppress leaf and panicle blast.

CONCLUSIONS: Overall, this study established a microbiome method for identifying the rice bacterial communities of agricultural significance, with capacity of rice disease management and/or growth promotion.},
}

@article {pmid41204050,
year = {2025},
author = {Li, J and Wang, S and Luo, P and Li, Z and Gopinath, D},
title = {Exploring the plausible genetic relationship of salivary and tongue microbiome with periodontitis: A mendelian randomization study.},
journal = {The Saudi dental journal},
volume = {37},
number = {10-12},
pages = {76},
pmid = {41204050},
issn = {1013-9052},
abstract = {Chronic periodontitis (CP) is associated with subgingival microbial dysbiosis and demonstrates specific microbial patterns, though definitive causal connections with microbiomes in distinct anatomical regions remain undetermined. Genome-wide association datasets for CP and oral microbial communities were sourced from a large European cohort and China National GeneBank DataBase (CNGBdb), respectively. Employing single-nucleotide polymorphisms (SNPs) as genetic instruments, Mendelian randomization (MR) analyses were conducted through the inverse-variance weighted (IVW) approach. Analysis methods were implemented through the 'TwoSampleMR' package (v0.6.4) in R software. Sensitivity analyses were performed to validate the robustness of the findings and mitigate the occurrence of horizontal pleiotropy. The MR analyses revealed three salivary bacterial taxa, Neisseria meningitidis (OR = 0.67, 95% CI, 0.49-0.98), Streptococcus vestibularis (OR = 0.74, 95% CI, 0.56-0.98), and Lancefieldella unclassified (OR = 0.68, 95% CI, 0.52-0.91) to be significantly associated with a reduced risk of CP (p < 0.05). In contrast, tongue microbial taxa Solobacterium unclassified (OR = 1.45, 95% CI, 1.04-2.04), Fusobacterium sp000235465 (OR = 1.40, 95% CI, 1.02-1.94), and Haemophilus parainfluenzae (OR = 1.56, 95% CI, 1.12-2.18) were associated with an increased CP risk (p < 0.05). No evidence of heterogeneity and directional pleiotropy was noted for these associations. This study highlights the association between specific salivary and tongue microbial taxa and CP, providing mechanistic linkages into the plausible relationship. It also suggests that some microbial taxa may be further explored as indicators for risk-stratified preventive measures and novel targets for precision prebiotics and therapies.},
}

@article {pmid41204024,
year = {2025},
author = {Mileng, K and Mani, S and Bezuidenhout, JJ and Mokgokong, PS and Ramatla, TA and Thekisoe, OMM and Lekota, KE},
title = {Bacterial Communities Harboured by Amblyomma Hebraeum Infesting Small Stock in Mahikeng city, South Africa.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {118},
pmid = {41204024},
issn = {1432-184X},
support = {GUN: CSUR23030681021//National Research Foundation/ ; },
mesh = {Animals ; South Africa ; *Bacteria/classification/genetics/isolation & purification ; Goats/parasitology/microbiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Sheep/parasitology ; *Amblyomma/microbiology ; *Tick Infestations/veterinary/parasitology/epidemiology ; *Goat Diseases/parasitology/microbiology/epidemiology ; Phylogeny ; *Sheep Diseases/parasitology/microbiology/epidemiology ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing ; },
abstract = {Ticks are important vectors of pathogens affecting livestock productivity and public health, yet their bacterial communities remain poorly characterized in many parts of South Africa. This study investigated the bacterial diversity and potential pathogenic bacterial etiology associated with Amblyomma hebraeum ticks collected from sheep and goats in Mahikeng, North West province. A total of 168 adult ticks were sampled across four villages. Microbiome profiling was performed using high-throughput sequencing of the V3-V4 hypervariable regions of the 16S rRNA gene on the Illumina MiSeq platform. High-throughput 16S rRNA sequencing revealed 16,193 ASVs in goat-derived ticks and 16,510 ASVs in those from sheep. Proteobacteria emerged as the dominant phylum across all samples, with ticks collected from goats showing a particularly high dominance of Rickettsia spp. (51.64% relative abundance), suggesting potential zoonotic risks. In contrast, ticks from sheep harboured significantly more diverse and evenly distributed bacterial communities, as indicated by Shannon (p = 0.0138) and Simpson (p = 0.0233) diversity indices, despite comparable species richness. A core microbiome comprising 1,374 ASVs (32.3%) was shared across all ticks, alongside 1,504 and 1,372 unique ASVs in goat- and sheep-derived ticks, respectively. Notably, several medically and veterinary-relevant genera, including Coxiella, Ehrlichia, Staphylococcus, Bacillus, Acinetobacter, Corynebacterium, and Streptococcus, were detected across both host groups. While total species richness was comparable between hosts, alpha diversity indices that account for evenness revealed host-based differences, and beta diversity patterns further showed clear separation of bacterial communities by host species. This study indicates that the host plays a crucial role as an ecological driver affecting the diversity of microbial communities associated with ticks. This study improves our understanding of the diversity, composition, and abundance of tick-associated microbiomes and pathogens in South African small ruminants. These insights support the development of microbiome-targeted strategies for detecting and controlling tick-borne diseases.},
}

Animals
South Africa
*Bacteria/classification/genetics/isolation & purification
Goats/parasitology/microbiology
*Microbiota
RNA, Ribosomal, 16S/genetics
Sheep/parasitology
*Amblyomma/microbiology
*Tick Infestations/veterinary/parasitology/epidemiology
*Goat Diseases/parasitology/microbiology/epidemiology
Phylogeny
*Sheep Diseases/parasitology/microbiology/epidemiology
DNA, Bacterial/genetics
High-Throughput Nucleotide Sequencing

@article {pmid41203821,
year = {2025},
author = {Young, JD and Pinnell, LJ and Wolfe, CA and Scott, MA and Lawrence, TE and Cavasin, JP and Ellis, JA and Langsten, KL and Richeson, JT and Morley, PS},
title = {Microbial communities and tight junction protein expression in the gastrointestinal tract of feedlot cattle.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {39055},
pmid = {41203821},
issn = {2045-2322},
mesh = {Animals ; Cattle ; *Tight Junction Proteins/metabolism/genetics ; *Gastrointestinal Microbiome ; *Gastrointestinal Tract/microbiology/metabolism ; RNA, Ribosomal, 16S/genetics ; Rumen/microbiology/metabolism ; Male ; Tight Junctions/metabolism ; Bacteria/genetics/classification ; },
abstract = {The gastrointestinal tract (GIT) of cattle plays a vital role in nutrient absorption, immune function, and microbial homeostasis. While the importance of the GIT microbiome and epithelial barrier integrity has been increasingly recognized, the typical composition of microbial communities and the expression of tight junction proteins (TJPs) in feedlot cattle remains poorly characterized. We investigated microbial community structure and TJP expression at three GIT sites: the rumen (RU), small intestine (SI), and large intestine (LI) in 21 finish-fed feedlot steers sourced from 21 commercial feedyards in the Texas Panhandle. Samples of luminal contents and GIT tissue were collected from each region, as well as feces and liver abscess material. Microbial communities were characterized using 16S rRNA gene sequencing. TJP gene expression was quantified by RT-qPCR using synthetic standards, and protein expression was evaluated by immunohistochemistry (IHC) with both computer-generated and pathologist-generated scoring. Microbial community structures varied primarily by GIT region rather than by individual animals raised at different locations. Nine bacterial families were identified as core microbiome members, with Lachnospiraceae being the most abundant across the GIT. TJP gene expression varied considerably by site, with RU having significantly lower Claudin 1, Claudin 2, and E-Cadherin expression than the SI and LI. IHC results paralleled qPCR findings, with region-specific patterns of protein localization and intensity. Computerized and pathologist-generated H-scores showed moderate agreement but differed notably between epithelial and lamina propria regions. This study provides a comprehensive baseline of microbial and host factors associated with gut health in a uniquely diverse population of feedlot cattle. The identification of regional microbial communities and distinct TJP expression patterns offers foundational insights into gastrointestinal physiology and barrier function. This work establishes baseline data to support future investigations into the relationships among microbial ecology, epithelial barrier function, and cattle health and productivity.},
}

Animals
Cattle
*Tight Junction Proteins/metabolism/genetics
*Gastrointestinal Microbiome
*Gastrointestinal Tract/microbiology/metabolism
RNA, Ribosomal, 16S/genetics
Rumen/microbiology/metabolism
Male
Tight Junctions/metabolism
Bacteria/genetics/classification

@article {pmid41203749,
year = {2025},
author = {Bowman, JP},
title = {Extensive fecal cast production and growth of Vibrionaceae in heat-stressed Atlantic salmon post-smolts.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {39064},
pmid = {41203749},
issn = {2045-2322},
mesh = {Animals ; *Salmo salar/microbiology/physiology ; *Feces/microbiology ; Gastrointestinal Microbiome ; *Vibrionaceae/growth & development/genetics/isolation & purification ; *Heat-Shock Response ; RNA, Ribosomal, 16S/genetics ; Hot Temperature ; Female ; },
abstract = {Atlantic salmon (Salmo salar) are known to reduce or cease voluntary feeding and show altered digesta consistency under heat stress. This study was performed to determine what bacterial species occur and to characterize bacterial taxa and quantify changes in gut microbial abundance under heat stress. Atlantic salmon (all female, 1.5 kg average weight) in seawater tanks at 15 °C were fed for 2 to 4 weeks. Tank temperatures were increased to a 19 °C "warm phase" until voluntary feeding abated at which point tank temperatures were cooled to 15 °C for 4 weeks. At the end of each temperature phase the fish were stripped of feces and microbiome profiles were determined using 16 S rRNA V1-V3 metabarcoding. The tank experiment was repeated three times in successive years. Abundances of bacteria were determined using qPCR. Vibrionaceae comprised most reads after the warm phase completed. The prominent levels of Vibrionaceae were accompanied by a large predominance of cast (sloughed intestinal mucosa) containing fecal samples. Quantitative PCR (qPCR) estimated fecal Vibrionaceae cell populations increased 1.9-3.4 log units/g after the warm phase. This population then decreased by 0.3-1.1 log units/g by the end of the 15 °C recovery phase. The gut Vibrionaceae and non-Vibrionaceae compositions in the separate trials were different each time. The results indicated heat stress induced inappetence corresponds to increased cast production accompanied by predominance of Vibrionaceae. The predominance of different bacteria in each trial could be partly due to the different initial abundances of taxa in the inputted smolt. Vibrionaceae colonizing the Atlantic salmon gut should be the focus of studies on the microbiology of thermally induced inappetence and dysbiosis in Atlantic salmon.},
}

Animals
*Salmo salar/microbiology/physiology
*Feces/microbiology
Gastrointestinal Microbiome
*Vibrionaceae/growth & development/genetics/isolation & purification
*Heat-Shock Response
RNA, Ribosomal, 16S/genetics
Hot Temperature
Female

@article {pmid41203701,
year = {2025},
author = {Lee, Y and Seo, J and Di Camillo, B},
title = {SHAP-based binarization enhances metataxonomic machine learning with application to gut microbiota of inflammatory bowel disease.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {39059},
pmid = {41203701},
issn = {2045-2322},
support = {IITP-2024-0044-1407//Korean Government [Ministry of Science and ICT (MSIT)]/ ; IITP-2024-0044-1407//Korean Government [Ministry of Science and ICT (MSIT)]/ ; DI_C_BIRD2020_01//Department of Information Engineering of the University of Padova/ ; },
mesh = {*Gastrointestinal Microbiome ; *Machine Learning ; Humans ; *Inflammatory Bowel Diseases/microbiology ; Biomarkers ; },
abstract = {Machine learning has been increasingly applied to microbiome data for biomarker discovery. However, microbiome datasets are typically high-dimensional, sparse, and correlated, which makes model training challenging and prone to overfitting. Previous studies have also reported that microbiome features exhibit binary-like characteristics, and that binarization does not necessarily reduce predictive performance. This observation motivated our work. Building on this idea, we propose a SHAP-based binarization pipeline. We first trained several machine learning models on raw continuous data and selected the best-performing model (random forest). Using SHAP values derived from the training set, we determined feature-specific thresholds that best separated positive and negative contributions. The dataset was then binarized using these thresholds and new models were trained on the transformed data. We evaluated this approach on gut microbiome abundance data (283 species, 220 genera, 1,569 individuals) to classify inflammatory bowel disease (IBD) versus healthy controls. The SHAP-based binarization consistently improved classification performance and interpretability compared with both continuous data and zero-threshold binarization. The best model's Matthews correlation coefficient increased from 0.884 to 0.928, with the largest improvements observed in non-tree-based models such as logistic regression and neural networks. SHAP summary plots also revealed clearer feature patterns, and biomarker rankings were more stable. In addition, the pipeline enabled us to identify a concise set of 17 microbial biomarkers associated with IBD. This study introduces a novel approach for microbiome data analysis by explicitly linking binarization thresholds to SHAP-derived feature contributions. Our approach was grounded in the observation of binary-like patterns revealed through SHAP values. Furthermore, although binarization inevitably raises concerns about information loss, our evaluation confirmed improvements not only in predictive performance but also in interpretability and biomarker stability, providing a broader validation of robustness. These findings highlight SHAP-based binarization as an effective strategy for high-dimensional microbiome data, with broad applicability and opportunities for future extension.},
}

*Gastrointestinal Microbiome
*Machine Learning
Humans
*Inflammatory Bowel Diseases/microbiology
Biomarkers