@article {pmid41298524,
year = {2025},
author = {Wimmer, BH and Moraïs, S and Amit, I and Tovar-Herrera, O and Tatli, M and Trautwein-Schult, A and Pfister, B and Zalk, R and Tödtli, P and Simoni, S and Lisibach, M and Levin, L and Becher, D and Bayer, EA and Medalia, O and Mizrahi, I},
title = {Spatial constraints drive amylosome-mediated resistant starch degradation by Ruminococcus bromii in the human colon.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-65800-1},
pmid = {41298524},
issn = {2041-1723},
abstract = {Degradation of complex dietary fiber by gut microbes is essential for colonic fermentation, short-chain fatty acid production, and microbiome function. Ruminococcus bromii is the primary resistant starch (RS) degrader in humans, which relies on the amylosome, a specialized cell-bound enzymatic complex. To unravel its architecture, function, and the interplay among its components, we applied a holistic multilayered approach: Cryo-electron tomography reveals that the amylosome comprises a constitutive extracellular layer extending toward the RS substrate. Proteomics demonstrates remodeling of its contents across different growth conditions, with Amy4 and Amy16 comprising 60% of the amylosome in response to RS. Structural and biochemical analyses reveal complementarity and synergistic RS degradation by these enzymes. We demonstrate that amylosome composition and RS degradation are regulated at two levels: structural constraints and expression-driven shifts in enzyme proportions enforce enzyme proximity, which allows R. bromii to fine-tune its adaptation to dietary fiber and shape colonic metabolism.},
}

@article {pmid41298521,
year = {2025},
author = {Reyes, A and Durán, C and Rodríguez-Otálora, S and Delgado Pugley, D and Iraola, G and Domínguez-Bello, MG and Lawley, TD and Tsukayama, P},
title = {A Latin American perspective on microbiome research.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66756-y},
pmid = {41298521},
issn = {2041-1723},
abstract = {The human gut microbiome plays a crucial role in human health, adapting and responding to changes in diet, environment, and lifestyle. However, current microbiome research is heavily biased toward high-income countries, leaving regions such as Latin America and the Caribbean (LAC) severely underrepresented. This imbalance limits our global understanding of microbial diversity and hinders the development of region-specific health interventions. In this Perspective, we discuss how LAC offers an exceptional opportunity for microbiome studies due to its unique ethnic diversity, rapid urbanization, distinct dietary traditions, and dual burden of infectious and chronic diseases. We highlight key findings from regional microbiome research, emphasizing the high diversity of ancestral microbial communities and the rapid shifts occurring in response to urbanization and globalization. To address existing disparities, we also introduce the Latinbiota Consortium, a collaborative network formed to strengthen local scientific capacity, ensure ethical and equitable research practices, promote data sovereignty, and foster inclusive participation by LAC researchers within global microbiome science. Through strategic investment and international collaboration, Latinbiota aims to preserve microbial diversity and ensure equitable participation in global microbiome science.},
}

@article {pmid41298497,
year = {2025},
author = {Nauta, KM and Gates, DR and Weiland, M and Mechan-Llontop, ME and Wang, X and Isaguirre, C and Gendjar, MR and Cooper, J and Barton, SF and Nguyen, KP and Sheldon, RD and Krawczyk, CM and Burton, NO},
title = {A noncanonical polyamine from bacteria antagonizes host mitochondrial function.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66499-w},
pmid = {41298497},
issn = {2041-1723},
support = {1DP2DK139569-01//U.S. Department of Health & Human Services | NIH | Office of Extramural Research, National Institutes of Health (OER)/ ; },
abstract = {Interactions between gut bacterial polyamines and intestinal cells have been proposed to contribute to inflammatory bowel diseases, but the underlying molecular mechanisms are often unclear. Here, we use a derivatization-based LC-MS approach and the model animal Caenorhabditis elegans to study microbiome-derived polyamine bioactivity. We show that aberrant polyamine metabolism in two diverse bacterial species (Escherichia coli K12 and Bacillus subtilis 168) can result in the accumulation of a noncanonical polyamine intermediate, N[1]-aminopropylagmatine (N[1]-APA). N[1]-APA is produced via spermidine synthase (SpeE) and is bioactive in C. elegans intestinal cells and mouse bone marrow macrophages. Specifically, bacterial N[1]-APA can be transported into intestinal cells via the polyamine transporter CATP-5, where it antagonizes C. elegans development and activates the mitochondrial unfolded protein response. N[1]-APA functions analogously to the deoxyhypusine synthase inhibitor GC7 in C. elegans and, like GC7, it antagonizes eIF5A hypusination and inhibits the alternative activation of mouse macrophages in vitro. Our results indicate that bacterial N[1]-APA is a bioactive metabolite that functions similarly to deoxyhypusine synthase inhibitors but has other unidentified targets that likely play roles in mitochondrial stress responses. We hypothesize that N[1]-APA production by the gut microbiome, caused by either high dietary agmatine or loss of agmatinase activity, might contribute to inflammatory bowel diseases.},
}

@article {pmid41298270,
year = {2025},
author = {Zou, J and Xu, H and Qin, B and Lan, C and Li, J and Zhang, B and Zhang, H and Guo, C and Chen, H and Fang, Z and Zhao, Q and Wang, W and Fang, C and Zhang, Z and Lin, W},
title = {Ratoon Season Rice Reduces Methane Emissions by Limiting Acetic Acid Transport to the Rhizosphere and Inhibiting Methanogens.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e07916},
doi = {10.1002/advs.202507916},
pmid = {41298270},
issn = {2198-3844},
support = {32001109//Nature Science Foundation of China/ ; 31871542//national Nature Science Foundation of China/ ; 31871556//national Nature Science Foundation of China/ ; 2017YFE0121800//National Key Research and Development Project of China/ ; 2018YFD0301105//National Key Research and Development Project of China/ ; BQW [2024]001//Innovative Talent Team in Rice Crop Science and Technology in Karst Mountainous Areas of Guizhou Province/ ; 2023//Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province/ ; (2023) 007//Key Laboratory of Functional Agriculture of Guizhou Provincial Higher Education Institutions/ ; Key Laboratory of Functional Agriculture of Guizhou Provincial Higher Education Institutions (//Chongqing Municipal Key Laboratory of Institutions of Higher Education/ ; Qianjiaoji//Chongqing Municipal Key Laboratory of Institutions of Higher Education/ ; (2023)007)//Chongqing Municipal Key Laboratory of Institutions of Higher Education/ ; Xiligongmi//Chongqing Municipal Key Laboratory of Institutions of Higher Education/ ; Innovative Talent Workstation of Guizhou Province(Qian-//Chongqing Municipal Key Laboratory of Institutions of Higher Education/ ; Ke//Chongqing Municipal Key Laboratory of Institutions of Higher Education/ ; -He-Platform-talent KXJZ(2024)038)//Chongqing Municipal Key Laboratory of Institutions of Higher Education/ ; (Qian-//Key Laboratory of Microbial Resources and Drug Development in Guizhou Province/ ; Ke//Key Laboratory of Microbial Resources and Drug Development in Guizhou Province/ ; -He YWZ(2024(004)//Key Laboratory of Microbial Resources and Drug Development in Guizhou Province/ ; },
abstract = {Rice paddies are a major, persistent source of atmospheric methane (CH4), emission rates depend on the partitioning of photosynthate carbon between the rice plant and the rhizosphere microbiome. Although ratoon season rice (RR) is shown to emit far less CH4 than main-crop rice (MC), the mechanisms have remained unresolved. This work conducts a 2-year field experiment in which RR is compared with MC and with late rice (LR) synchronized to the RR heading stage. Relative to MC and LR, RR lowers daily CH4 flux by 91%, raises daily grain yield by 34%-57%, and increases net economic return by 90%-136%. Mechanistically, [13]C-labelling reveals that RR diverted more newly fixed carbon to the grain and less to the rhizosphere, thereby restricting acetate availability for methanogens. Rhizosphere metagenomics show reduced abundance of Methanobacteriaceae and down-regulation of methanogenic genes in RR. This carbon-reallocation pattern is underpinned by an abscisic acid (ABA)-mediated interaction between OsCIPK2 and OsSWEET1A, which simultaneously curtailed carbon efflux from roots and enhanced grain filling. This study is the first to establish a comprehensive framework of "ABA regulation-carbon allocation-microbial function-emission reduction and efficiency enhancement." It provides targetable strategies for carbon allocation and microbial management within climate-smart rice farming systems.},
}

@article {pmid41298102,
year = {2025},
author = {Ammer-Herrmenau, C and Meier, R and Antweiler, KL and Asendorf, T and Cameron, S and Capurso, G and Damm, M and Dang, L and Frost, F and Hamm, J and Hoffmeister, A and Kocheva, Y and Meinhardt, C and Nawacki, L and Nunes, V and Panyko, A and Ruiz-Rebollo, ML and Flórez-Pardo, C and Phillip, V and Pukitis, A and Vaselane, D and Rinja, E and Sandru, V and Schaefer, A and Scholz, R and Seelig, J and Sirtl, S and Ellenrieder, V and Neesse, A},
title = {Gut microbiota predict development of postdischarge diabetes mellitus in acute pancreatitis.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-336715},
pmid = {41298102},
issn = {1468-3288},
abstract = {BACKGROUND: Postdischarge morbidity and mortality is high in acute pancreatitis (AP) and pathophysiological mechanisms remain poorly understood.

OBJECTIVES: We aim to investigate the composition of gut microbiota and clinical long-term outcomes of prospectively enrolled patients with AP to predict postdischarge complications.

DESIGN: In this long-term follow-up study, we analysed clinical and microbiome data of 277 patients from the prospective multicentre Pancreatitis-Microbiome As Predictor of Severity trial. The primary endpoint was the association of the microbial composition with postdischarge mortality, recurrent AP (RAP), progression to chronic pancreatitis, pancreatic exocrine insufficiency, diabetes mellitus (DM) and pancreatic ductal adenocarcinoma.

RESULTS: Buccal (n=238) and rectal (n=249) swabs were analysed by 16S rRNA and metagenomics sequencing using Oxford Nanopore Technologies. Median follow-up was 2.8 years. Distance-based redundancy analysis with canonical analysis of principal coordinates showed significant differences for β-diversity (Bray-Curtis) for postdischarge mortality (p=0.04), RAP (p=0.02) and DM (p=0.03). A ridge regression model including 11 differentially abundant species predicted postdischarge DM with an area under the receiving operating characteristic of 94.8% and 86.2% in the matched and entire cohort, respectively. Using this classifier, a positive predictive value of 66.6%, a negative predictive value of 96% and an accuracy of 95% was achieved.

CONCLUSION: Our data indicate that the admission microbiome of patients with AP correlates with postdischarge complications independent from multiple risk factors such as AP severity, smoking or alcohol. Microbiota at admission show excellent capacity to predict postdischarge DM and may thus open new stratification tools for a tailored risk assessment in the future.

TRIAL REGISTRATION NUMBER: NCT04777812.},
}

@article {pmid41298101,
year = {2025},
author = {Liu, CS and Merrick, B and Taboun, ZS and Mullish, BH and Goldenberg, SD and Terveer, EM and Porcari, S and Bradbury, RS and Ianiro, G and Ng, SC and , and Kao, D and Kuijper, E},
title = {Towards optimising and standardising donor screening for faecal microbiota transplantion.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-336532},
pmid = {41298101},
issn = {1468-3288},
abstract = {Rigorous donor screening is fundamental for the safe and effective delivery of faecal microbiota transplantion (FMT) services, whether in the treatment of Clostridioides difficile infection or within microbiome intervention clinical trials. Donor screening is of paramount importance given the potential risk of pathogen transmission-a feared complication. While rare in practice, documented cases of FMT-associated infections have resulted in significant morbidity and even mortality. Despite the importance of screening, evidence-based approaches to developing donor-screening protocols are lacking. Inadequate screening for transmissible pathogens may lead to infections in recipients, while overly cautious screening for pathogens with negligible transmission potential could strain healthcare resources and unnecessarily exclude donors, who are already in limited supply. This review aimed to evaluate the evidence underpinning current FMT donor screening protocols. We began by comparing protocols from major FMT guidelines and manufacturers, highlighting their differences in lists of screened pathogens, laboratory assays and clinical characteristics used for donor selection. We critically appraised the existing literature on transmission dynamics for pathogens. These findings were incorporated into a Delphi process with an expert panel group to develop a rational and streamlined screening approach. We further emphasised the importance of maintaining transparency with regard to donor recruitment, screening, monitoring and traceback record keeping. Finally, we explored future directions in donor screening, including approaches to monitoring emerging pathogens and the potential for integration of new technologies, such as metagenomic assays, to enhance and refine donor selection.},
}

@article {pmid41297980,
year = {2025},
author = {Maznyczka, A and De Backer, O and Généreux, P and Blackman, DJ and Pilgrim, T},
title = {The Inflammatory Response to Transcatheter Aortic Valve Replacement.},
journal = {JACC. Cardiovascular interventions},
volume = {18},
number = {22},
pages = {2685-2700},
doi = {10.1016/j.jcin.2025.09.023},
pmid = {41297980},
issn = {1876-7605},
mesh = {Humans ; *Transcatheter Aortic Valve Replacement/adverse effects/instrumentation/mortality ; Treatment Outcome ; Risk Factors ; *Inflammation/immunology/mortality/epidemiology/therapy/diagnosis/prevention & control ; Inflammation Mediators/blood/metabolism/immunology ; *Aortic Valve/surgery/physiopathology/immunology ; Risk Assessment ; Anti-Inflammatory Agents/therapeutic use ; Heart Valve Prosthesis ; *Aortic Valve Stenosis/surgery/physiopathology/diagnostic imaging/mortality ; },
abstract = {Inflammation is common in response to transcatheter aortic valve replacement (TAVR), resulting from endothelial damage, procedure-related hypoperfusion, and immunogenicity against the bioprosthesis. The systemic inflammatory response after TAVR comprises a spectrum ranging from asymptomatic biomarker elevation to dramatic clinical manifestations. Although local inflammation post-TAVR is part of physiological healing, a hyperinflammatory response increases the risk for conduction disturbances, new-onset atrial fibrillation, acute kidney injury, prolonged hospitalization, mortality, and subclinical leaflet thrombosis. Unfavorable monocyte and T helper cell signatures can predispose to worse outcomes in connection with hyperinflammation. Strategies are needed to control key drivers of hyperinflammation after TAVR (eg, avoiding prolonged hypotension during transcatheter aortic valve deployment, periprocedural colchicine or glucocorticoids, targeted monoclonal antibodies, a healthy gut microbiome) and to identify patients in whom modulation of inflammatory pathways may optimize outcomes. This review provides a detailed description of the epidemiology, pathophysiology, and consequences of the inflammatory response to TAVR and discusses emerging treatment pathways.},
}

Humans
*Transcatheter Aortic Valve Replacement/adverse effects/instrumentation/mortality
Treatment Outcome
Risk Factors
*Inflammation/immunology/mortality/epidemiology/therapy/diagnosis/prevention & control
Inflammation Mediators/blood/metabolism/immunology
*Aortic Valve/surgery/physiopathology/immunology
Risk Assessment
Anti-Inflammatory Agents/therapeutic use
Heart Valve Prosthesis
*Aortic Valve Stenosis/surgery/physiopathology/diagnostic imaging/mortality

@article {pmid41297880,
year = {2025},
author = {Chue, KM and Wong, SH and Zuo, T and Ali, Y},
title = {The Role of the Gut Non-Bacterial Microbiome (Virome, Mycobiome, Archaeome) and its Impact on Obesity.},
journal = {Molecular metabolism},
volume = {},
number = {},
pages = {102289},
doi = {10.1016/j.molmet.2025.102289},
pmid = {41297880},
issn = {2212-8778},
abstract = {The epidemic of obesity and metabolic syndrome is a major public health concern internationally. There is increasing knowledge and research in areas of appetite regulation and drivers of obesity but there is still a gap on how the interactomes are altered in a metabolically dysregulated human body. The human microbiome has been implicated in the pathogenesis of obesity. While the association of gut bacteriome dysbiosis is well described in obesity and metabolic syndrome, there is a lack of an integrative understanding about the roles of the non-bacterial microbiome (virome, mycobiome, and archaeome) in the pathogenesis and protection of obesity and metabolic syndrome. Accumulating studies have revealed that the non-bacterial microbes in the gut, including viruses/ phages, fungi, and archaea, are profoundly altered in obesity, and impact host adiposity and physiology in nuanced manners. In this review, we aim to provide a comprehensive view on the role and the mechanisms of the gut virome, mycobiome, and archaeome in obesity. These insights will shed light on the translational value as well as the future research directions for harnessing the gut non-bacterial microbial entities in the therapeutics and prevention of metabolic diseases.},
}

@article {pmid41297775,
year = {2025},
author = {Ferrini, A and He, M and Mont, MA and Goodman, SB and Parvizi, J},
title = {Osteonecrosis of the femoral head: A Dysbiotic Condition?.},
journal = {The Journal of arthroplasty},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.arth.2025.11.044},
pmid = {41297775},
issn = {1532-8406},
abstract = {Osteonecrosis of the femoral head (ONFH) is a progressive and disabling condition of the hip joint that primarily affects young and active individuals, leading to progressive collapse of subchondral bone and often secondary arthritis. Despite extensive investigation, the precise etiology often remains unclear. While high-dose corticosteroids, chronic alcohol ingestion, and smoking are known associated risk factors, approximately 20 to 30% of ONFH cases are classified as idiopathic. Recently, the concept of gut dysbiosis, i.e., disruption of the normal intestinal microbial balance, has gained increasing attention due to its systemic immunologic and metabolic implications. Dysbiosis is associated with an increase in gut permeability, leading to the translocation of bacteria and their metabolic products, including lipopolysaccharides and short-chain fatty acids (SCFAs), into the systemic circulation. This may stimulate proinflammatory cascades throughout the body, including the joints, initiating a bone remodeling process. Emerging evidence from preclinical and human research suggests that specific gut microbiota taxa may influence key mechanisms involved in the pathogenesis of ONFH. Additionally, early findings support the therapeutic potential of microbiota-targeted therapies such as probiotics, SCFAs-enriched diets, and fecal microbiota transplantation (FMT). Although a growing number of descriptive studies support this link, the current evidence remains associative rather than causal, as no longitudinal cohort studies have confirmed this relationship. Future investigations are needed to establish causality between gut dysbiosis and ONFH. To our knowledge, this review offers the first comprehensive synthesis of the literature aiming to explore current evidence and the potential link between gut dysbiosis and ONFH, highlighting future directions for microbiome-based therapeutic interventions.},
}

@article {pmid41297668,
year = {2025},
author = {Liu, Y and Lv, H and Zhang, H and Li, H and Wang, A and Yu, S and He, Q and Chen, S and Wang, J and Ran, X and Cao, G},
title = {The protective role of intestinal alkaline phosphatase in inflammatory bowel disease-associated non-alcoholic fatty liver disease.},
journal = {Life sciences},
volume = {},
number = {},
pages = {124113},
doi = {10.1016/j.lfs.2025.124113},
pmid = {41297668},
issn = {1879-0631},
abstract = {BACKGROUND: Inflammatory bowel disease (IBD) is a chronic and progressive inflammatory condition characterized by weight loss as a prominent feature. Non-alcoholic fatty liver disease (NAFLD), typically linked to obesity and metabolic dysregulation, is increasingly recognized as being influenced by the gut-liver axis. Notably, IBD patients exhibit a heightened susceptibility to NAFLD, although the underlying mechanisms remain poorly understood. Intestinal alkaline phosphatase (IAP), an endogenous enzyme, plays a critical role in preventing intestinal bacterial translocation. We hypothesized that IAP may serve as a potential therapeutic agent for mitigating IBD-associated NAFLD.

METHODS: An IBD model was established using three cycles of 2 % dextran sulfate sodium (DSS) administration. Mice were subsequently treated with L-phenylalanine or IAP. The activity of stool IAP, gut microbiota composition, hepatic lipid accumulation, inflammatory markers, and gut microbiome diversity were assessed.

RESULTS: DSS treatment markedly reduced IAP levels. Suppression of IAP significantly increased gut permeability and exacerbated hepatic inflammation and lipid deposition. Conversely, IAP supplementation restored these parameters, improved gut microbial diversity, and normalized microbiota composition. However, IAP failed to ameliorate hepatic inflammation and lipid accumulation in Toll-like receptor 4 (TLR4) knockout mice.

CONCLUSION: Deficiency in endogenous IAP contributes to the onset of NAFLD in the context of IBD. Oral IAP supplementation enhances gut barrier integrity, stabilizes gut microbiota, and prevents NAFLD development in IBD through a TLR4-dependent mechanism.},
}

@article {pmid41297633,
year = {2025},
author = {Daiy, KE and Bertacchi, V and Choy, CC and Unasa, F and Savusa, K and Abraham, J and Soti-Ulberg, C and Naseri, T and Williams, JE and McGuire, MA and McGuire, MK and Valeggia, CR and Hawley, NL},
title = {Associations among maternal nutrient intake and infant fecal and human milk microbiomes in exclusively breastfeeding Samoan mother-infant dyads.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2025.11.015},
pmid = {41297633},
issn = {1541-6100},
abstract = {BACKGROUND: Human diet is changing rapidly around the world, and literature suggests that diet impacts human microbiomes. It is unclear whether maternal nutrient intake is associated with the milk and infant gastrointestinal (GI; gut) microbiomes in nutritionally-transitioning populations where wide dietary variability may uniquely shape microbial exposures and responses.

OBJECTIVE: We examine how maternal nutrient intake is associated with the human milk and infant fecal microbiomes in Samoa, a nutritionally transitioning nation.

METHODS: Exclusively breastfeeding Samoan mother-infant dyads (n=100) were recruited between 2-4 months postpartum across urban, peri-urban and rural regions to capture the nutrition transition. Daily energy-adjusted maternal nutrient intake was assessed using 24-hour diet recalls. Human milk and infant fecal microbiomes were characterized through 16S rRNA gene sequencing.

RESULTS: Total lipid (β = 0.002, p = 0.037) and saturated fatty acid intakes (β = 0.005, p = 0.020) were positively associated with evenness in milk, whereas protein intake was positively associated with richness (β = 0.232, p = 0.010) and Stenotrophomonas (β = 0.001, q = 0.022) in milk. Polyunsaturated fatty acid intake was positively associated with Shannon diversity (β = 0.034, p = 0.023), evenness (β= 0.007, p = 0.011), and Clostridium (β = 0.006, q = 6.904 x 10[-5]) in infant feces. Fiber intake was negatively associated with Shannon diversity (β = -0.023, p = 0.008) and evenness (β = -0.004, p = 0.023) in infant feces. Nutrient intake was not associated with overall bacterial compositions of either milk or infant feces (p>0.05).

CONCLUSION: In Samoa, maternal nutrient intake is linked with the diversity and individual taxa of milk and infant feces but was not associated with overall microbiome composition. Effects of changing maternal diet on maternal and infant microbiomes may therefore contribute to health outcomes associated with the nutrition transition.},
}

@article {pmid41297540,
year = {2025},
author = {Agirman, G and Quicho, MNB and Connelley, KK and Zhang, X and Lynch, JB and Ha, SM and Schmidt, HM and Özcan, E and Liang, AX and Yu, KB and Ahn, IS and Qian, C and Paramo, J and Zhang, S and Espinoza, A and Turnbaugh, PJ and de Aguiar Vallim, TQ and Yang, X and Church, A and Hsiao, EY},
title = {The microbial metabolite imidazole propionate modulates hypothalamic activity and stress-induced behaviors.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.10.019},
pmid = {41297540},
issn = {1934-6069},
abstract = {Metabolic disorders are associated with gut microbiome imbalance, which can have additional physiological effects. The microbial metabolite imidazole propionate (ImP) is elevated in type 2 diabetes and has been linked to exacerbated metabolic dysfunctions. Here, we show that bacteria-produced ImP can enter the bloodstream and modulate brain activity and behavior. Elevated circulating ImP reaches the brain, leading to altered neuronal gene expression in the hypothalamus, disrupted GABAergic/glutamatergic signaling, and stress-related behaviors. Similarly, colonization with ImP-producing Eggerthella lenta elevates behavioral and molecular stress features. In a mouse model of type 2 diabetes, the gut microbiome shows greater capacity to generate ImP, leading to elevated systemic levels associated with heightened stress responses. In humans, higher ImP levels are associated with reduced hypothalamic reactivity to food cues, impaired stress coping, and increased emotional eating. Overall, these findings establish ImP as a microbial metabolite that links gut dysbiosis to altered hypothalamic function and stress in metabolic disease.},
}

@article {pmid41297400,
year = {2025},
author = {Chen, S and Liu, Q and Li, D},
title = {Engineering the composting microbiome with a synthetic microbial community to accelerate lignocellulose degradation and humus synthesis.},
journal = {Journal of environmental management},
volume = {396},
number = {},
pages = {128088},
doi = {10.1016/j.jenvman.2025.128088},
pmid = {41297400},
issn = {1095-8630},
abstract = {Bioaugmentation with synthetic microbial communities (SynComs) presents a promising engineering strategy to overcome the bottleneck of lignocellulose recalcitrance in organic waste valorization. However, the mechanisms by which SynComs modulate indigenous microbial networks and steer metabolic fluxes remain elusive. Here, we deconstruct these mechanisms by investigating the impact of a rationally designed five-member bacterial-fungal SynCom on the co-composting of cattle manure and mulberry branches. Through an integrated multi-omics approach, we reveal that SynCom inoculation acts as a potent ecological engineer, accelerating the process by significantly elevating pile temperatures and shortening the maturation period by accelerating entry into the maturation phase by approximately 7 days. Compared with the control, the SynCom treatment enhanced the overall degradation rates of lignin, cellulose, and hemicellulose by 19.3 %, 7.9 %, and 12.0 %, respectively, and boosted humus content by 34.4 %. Metagenomics revealed that the SynCom profoundly restructured the native microbiome, enriching for key functional genera such as Thermobifida and Actinomadura. This engineered community possessed an enhanced genetic toolkit, with a significantly increased abundance of crucial carbohydrate-active enzymes (CAZymes), including cellulases (GH5, GH12), hemicellulases (CE1, CE3), and lignin-modifying auxiliary activity enzymes (AA1, AA6). Untargeted metabolomics further identified a distinct metabolic footprint in the SynCom treatment, characterized by the enrichment of key humification precursors like protocatechuic acid and sinapic acid. Integrated Procrustes and correlation analyses confirmed a tight coupling between the engineered microbiome, its functional gene repertoire and metabolic output. This study deciphers the multi-layered mechanism by which a designed SynCom enhances biowaste valorization and provides a mechanistic blueprint for engineering microbial consortia for advanced biotechnology applications in sustainable agriculture.},
}

@article {pmid41297327,
year = {2025},
author = {Fuad, MTI and Dong, Y and Li, Z and Ge, M and Sharifuzzaman, SM and Liu, X and Zhang, X and Xu, Q},
title = {Seasonal gut microbiota and functional dynamics in brittle star (Ophiothrix exigua) from the Yellow Sea, China.},
journal = {Marine environmental research},
volume = {213},
number = {},
pages = {107734},
doi = {10.1016/j.marenvres.2025.107734},
pmid = {41297327},
issn = {1879-0291},
abstract = {The gut microbiota forms a complex symbiotic community that performs essential functions for the host, including metabolism, nutrient absorption, and environmental adaptation, while being shaped by both environmental and intrinsic host factors. This study represents the first comprehensive investigation of seasonal gut microbiota diversity in brittle stars, examining Ophiothrix exigua from the Yellow Sea using full-length 16S rRNA gene metabarcoding. A total of 565 amplicon sequence variants were identified from gut samples, distributed across 20 phyla, 135 genera, and 46 species. The dominant phyla included Proteobacteria, and Spirochaetota, with Salinispira identified as the core genus. Seasonal variations in microbiota diversity were evident, with Caulobacter predominating in summer, and Kistimonas and Trichococcus driving winter community shift. Corresponding seasonal changes in gut microbiota functions and functional pathways were observed. Fatty acid biosynthesis pathways were enriched in winter, while aromatic compound degradation pathways showed elevated activity in summer. Although seawater microbiota exerted relatively minor influence on gut microbial diversity, correlations with abiotic factors such as pH were observed. This study highlights the intricate relationship between gut microbiota, environmental microbiota, and abiotic factors in shaping the seasonal gut microbiota diversity of O. exigua, contributing to a better understanding of the host-microbiome ecology of invertebrates.},
}

@article {pmid41297120,
year = {2025},
author = {Rajbhandari, RM and Shrestha, S and Manandhar, P and Napit, R and Sadaula, A and Chaudhary, A and Raut, R and Gortázar, C and Alves, PC and de la Fuente, J and Queirós, J and Forcina, G and Karmacharya, D},
title = {Comparing the respiratory tract microbiome in captive elephants and humans in Chitwan National Park: Implications for conservation medicine.},
journal = {Comparative immunology, microbiology and infectious diseases},
volume = {125},
number = {},
pages = {102422},
doi = {10.1016/j.cimid.2025.102422},
pmid = {41297120},
issn = {1878-1667},
abstract = {The study of gut microbiome in both animals and humans living in proximity has proven crucial in understanding their coevolution, the potential for microbial transfer and the dynamics behind various diseases. Similarly, the investigation of respiratory microbiomes has been gaining popularity due to its significance and impact on respiratory health. Here, we use 16S rRNA metabarcoding to explore the respiratory microbiome of captive Asian elephants (Elephas maximus) and their mahouts (i.e., trainers and handlers) in Chitwan National Park (Nepal), with local villagers residing out of the protected area acting as control. Sputum samples were collected to characterize their bacterial composition, while its functional profile was inferred with PICRUSt2. Additionally, the occurrence of genera hosting potentially pathogenic ESKAPE-E species was evaluated. Our findings revealed high similarity in the bacterial and functional composition of the respiratory microbiome of elephants and mahouts, with Bacillota and Pseudomonadota emerging as the most abundant phyla across all host categories and the controls displaying the highest diversity. A striking difference was observed in relation to the family Bacillaceae that dominated the microbial composition of both mahouts and elephants but not controls. Genera hosting potentially pathogenic ESKAPE-E bacteria were found in all host categories, which underscores the need for in-depth analyses to identify the species involved. Our study delivers valuable insights in the respiratory microbial community of both Asian elephants and humans, thus laying the basis for further investigations on their diversity and function, unveiling their role in respiratory health of both host species.},
}

@article {pmid41297027,
year = {2025},
author = {Palanisamy, H and Vidyalakshmi, S},
title = {Deciphering the Interrelation of Gut Microbiota and BMI in Atherosclerosis: A Metagenomic Approach.},
journal = {Canadian journal of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1139/cjm-2025-0075},
pmid = {41297027},
issn = {1480-3275},
abstract = {Atherosclerotic Cardiovascular Disease (ASCVD) is a global health concern, leading to higher rates of morbidity and mortality. Gut microbial dysbiosis significantly contributes to obesity related ASCVD. However the interrelation of gut microbiome in driving obesity or overweight mediated ASCVD has not been sufficiently investigated. To unravel this complex interplay, we have compared the gut microbial shotgun metagenome data of ASCVD subjects across normal BMI (Body Mass Index) and overweight/obese (OW/OB) BMI categories. We identified a distinct gut microbial composition and function in normal and OW/OB ASCVD subjects. Using gut microbial abundance, a machine learning model was built to predict ASCVD in the normal and OW/OB samples. The gut microbiome based signature for ASCVD discrimination was achieved with an AUC of 0.87 and 0.83 for distinguishing control and ASCVD in normal and OW/OB BMI groups respectively. In addition, we have also identified that Pseudoflavonifractor capillosus could act as a prognostic organism in identifying OW/OB associated ASCVD. Therefore, an appropriate diet could modifying the ASCVD contributing gut microbiome, hence minimizing the risk of ASCVD in OW/OB individuals.},
}

@article {pmid41296938,
year = {2025},
author = {Molinero, N and Montero-Atalaya, M and Méndez, L and Roldán, M and Cortés, IP and Ruhland, S and Bartolomé, B and Medina, I and Moreno-Arribas, MV},
title = {The Multinutrient Fortasyn Connect Influences Gut Microbiota and Intestinal Function in Early Alzheimer's Disease.},
journal = {Aging and disease},
volume = {},
number = {},
pages = {},
doi = {10.14336/AD.2025.1176},
pmid = {41296938},
issn = {2152-5250},
abstract = {Nutritional supplementation is emerging as a promising strategy to support clinical management of early Alzheimer's disease (AD), partly through modulation of the intestinal microbiome via the microbiota-gut-brain axis. This study investigated the impact of Fortasyn Connect (Souvenaid[®]), a multinutrient formulation, on gut microbiota using a dual approach: i) a dynamic gastrointestinal simulator (simgi[®]) inoculated with feces from AD patients, and ii) an observational study involving early-stage AD patients (n = 22) receiving or not the supplement. The in vitro model provided a direct, host-independent assessment of microbiota responses, showing increased Bifidobacterium and Lactobacillus levels, alongside enhanced short-chain fatty acid (SCFA) production. In patients, supplementation was associated with higher fecal abundance of Bifidobacterium and Christensenellaceae, reduced inflammatory markers (calprotectin and myeloperoxidase), and increased butyrate levels. Fecal lipidomic and proteomic analyses indicated improved lipid digestion, increased secretory IgA, and modulation of host proteins linked to gut-brain homeostasis. Systemically, elevated levels of iron, folate, and vitamin B12 were also observed. For the first time, this study shows that supplements such as Fortasyn Connect can beneficially modulate the gut ecosystem and related immune-metabolic pathways in early AD, thereby targeting disease-relevant mechanisms through the gut-brain axis, in the context of aging.},
}

@article {pmid41296882,
year = {2025},
author = {Guse, K and Rose, T and Pietri, JE},
title = {Diet has minimal effect on Salmonella Typhimurium infection in the gut of a cockroach vector despite altering the microbiome.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0157025},
doi = {10.1128/aem.01570-25},
pmid = {41296882},
issn = {1098-5336},
abstract = {UNLABELLED: The German cockroach, Blattella germanica, can harbor and transmit enteric human pathogens, including Salmonella enterica serovar Typhimurium. German cockroaches are omnivores that subsist on highly varied diets in the field, in contrast to most arthropod vectors. Diet plays an important role in shaping the gut microenvironment across a range of animals, which can in turn affect numerous aspects of physiology, including the ability to resist infection. Yet, the impact of diet on the ability of cockroaches to maintain and transmit pathogens had not been investigated previously. Here, we tested the hypothesis that dietary differences among otherwise identical populations of B. germanica could lead to differences in vector competence for S. Typhimurium. Cockroaches were maintained on three defined formulated diets with distinct macronutrient profiles for 10 days. Food consumption was monitored during this period, and the gut microbiome was profiled by 16S rRNA amplicon sequencing. The cockroaches were then orally infected with S. Typhimurium, and pathogen loads in the gut and excreta were quantified. Cockroaches equally consumed formulated high-protein, high-fat, and high-carbohydrate diets in no-choice assays. Furthermore, as expected, some significant differences in microbiome composition and diversity were observed between groups of cockroaches maintained on different diets. However, despite the effects on the microbiome, no significant diet-dependent differences in the load of S. Typhimurium maintained in the gut or shed in the excreta were observed. Although the results provide evidence that the dietary macronutrient profile is not a major contributor to vector competence, the possibility that other natural diets could influence pathogen infection and transmission dynamics is not ruled out by this study.

IMPORTANCE: German cockroaches are one of the most common structural pests worldwide, while Salmonella enterica serovar Typhimurium is an emerging human pathogen accounting for a significant portion of the global burden of enteric disease. Understanding the factors that contribute to the ability of cockroaches to transmit pathogens is important for infection prevention, but these remain almost entirely unknown. Here, we provide new insight into the variables involved in the vector competence of cockroaches.},
}

@article {pmid41296881,
year = {2025},
author = {Mayer, MJ and Sayavedra, L and Gotts, K and Wong, N and Whiley, H and Barham, M and Narbad, A},
title = {Human gut strains of Desulfovibrio piger exhibit spontaneous induction of multiple prophages.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0191725},
doi = {10.1128/aem.01917-25},
pmid = {41296881},
issn = {1098-5336},
abstract = {UNLABELLED: Sulfate-reducing bacterium Desulfovibrio piger is a common member of the human gastrointestinal microbiome, associated with inflammatory conditions but also prevalent in healthy individuals. This suggests that lifestyle factors may shape its ecological role. We investigated prophage carriage and release in three new D. piger strains from healthy donors and strain FI11049 from a patient with ulcerative colitis. Sequencing revealed a larger genome in strain FI11455 (3.096 Mb) compared to FI11311 (2.985 Mb) and FI11458 (2.838 Mb), including a 154 kb megaplasmid which contained an 87 kb section with high similarity to the chromosome of strain FI11311, suggesting horizontal gene transfer between chromosomes and plasmids. This section encoded genes involved in DNA replication, transcription, and recombination, as well as protein folding and modification, defense, and phage proteins. Strain FI11049 showed less than 95% similarity to other D. piger strains but shared similar prophages with them. Each strain carried four to five predicted prophages, ranging from 30 to 60 kb, which clustered into four groups, with at least three groups per strain. Although the prophages had no nucleotide similarity to known phages, genes for lysis, integration, regulation, and structural proteins were identified, and three groups contained Mu-like proteins. Electron microscopy and PCR of mitomycin C-induced supernatants confirmed the release of tailed bacteriophage particles and capsids of multiple prophages. Similar results were demonstrated from uninduced samples, indicating spontaneous prophage release. Host defense systems were widespread, and cross-infections failed to identify suitable hosts in related strains and species. This is the first evidence of prophage release in gut-associated Desulfovibrio, with implications for gene transfer in the gut.

IMPORTANCE: Gastrointestinal health has a significant impact on quality of life, and increasing profiling of the gut microbiome is identifying key players involved in disease states. However, evidence of the association of sulfate-reducing bacteria with pathologies, such as inflammatory bowel disease and colorectal cancer, conflicts with their prevalence in healthy subjects. Investigating the ecology of D. piger in the gut may be key to answering if and why it can be harmful and could inform future interventions. Here, we show that gut-associated D. piger strains carry multiple prophages, some of which are spontaneously released as bacteriophage particles in culture. Our results pave the way for future work to understand prophage release in gut conditions and its effects on D. piger populations.},
}

@article {pmid41296785,
year = {2025},
author = {Fonseca-Garcia, C and Pettinga, D and Caddell, D and Ploemacher, H and Louie, K and Bowen, BP and Park, J and Sanchez, J and Zimic-Sheen, A and Traxler, MF and Northen, TR and Coleman-Derr, D},
title = {Enrichment of root-associated Streptomyces strains in response to drought is driven by diverse functional traits and does not predict beneficial effects on plant growth.},
journal = {PLoS biology},
volume = {23},
number = {11},
pages = {e3003526},
doi = {10.1371/journal.pbio.3003526},
pmid = {41296785},
issn = {1545-7885},
abstract = {The genus Streptomyces has consistently been found enriched in drought-stressed plant root microbiomes, yet the ecological basis and functional variation underlying this enrichment at the strain and isolate level remain unclear. Using two 16S rRNA sequencing methods with different levels of taxonomic resolution, we confirmed drought-associated enrichment (DE) of Streptomyces in field-grown sorghum roots and identified five closely related but distinct amplicon sequence variants (ASVs) belonging to the genus with variable drought enrichment patterns. From a culture collection of sorghum root endophytes, we selected 12 Streptomyces isolates representing these ASVs for phenotypic and genomic characterization. Whole-genome sequencing revealed substantial variation in gene content, even among closely related isolates, and exometabolomic profiling showed distinct metabolic responses to media supplemented with drought- versus well-watered root tissue. Traits linked to drought survival, including osmotic stress tolerance, siderophore production, and carbon utilization, varied widely among isolates and were not phylogenetically conserved. Using a broader panel of 48 Streptomyces, we demonstrate that DE scores, determined through mono-association experiments in gnotobiotic sorghum systems, showed high variability and lacked correlation with plant growth promotion. Pangenome-wide association identified orthogroups involved in osmolyte transport (e.g., proP) and membrane biosynthesis (e.g., fabG) as positively associated with DE, though most associations lacked phylogenetic signal. Collectively, these results demonstrate that Streptomyces DE is not a conserved genus-level trait but is instead strain-specific and functionally heterogeneous. Furthermore, DE in the root microbiome was shown not to predict beneficial effects on plant growth. This work underscores the need to resolve functional traits at the strain level and highlights the complexity of microbe-host-environment interactions under abiotic stress.},
}

@article {pmid41296667,
year = {2025},
author = {Huang, L and Wang, L and Nong, H and Liu, B and Li, Y},
title = {Pharmacological Intervention for Refractory Biofilm Infection After Hemipelvic Replacement Surgery: Multidisciplinary Management of a Case of Giant Cell Tumor of Bone.},
journal = {The American journal of case reports},
volume = {26},
number = {},
pages = {e949210},
doi = {10.12659/AJCR.949210},
pmid = {41296667},
issn = {1941-5923},
mesh = {Humans ; Female ; Adult ; *Biofilms/drug effects ; *Prosthesis-Related Infections/drug therapy/microbiology/therapy ; *Anti-Bacterial Agents/therapeutic use ; *Giant Cell Tumor of Bone/surgery ; Vancomycin/therapeutic use ; Debridement ; *Bone Neoplasms/surgery ; *Pelvic Bones/surgery ; *Staphylococcal Infections/drug therapy ; Pseudomonas Infections/drug therapy ; Pseudomonas aeruginosa ; Rifampin/therapeutic use ; },
abstract = {BACKGROUND Periprosthetic joint infection (PJI) is a potentially catastrophic complication after orthopedic surgery. Biofilm formation and infection with multidrug-resistant pathogens significantly increase the difficulty of achieving successful treatment. CASE REPORT A 36-year-old woman presented with a 6-month history of left hip pain. Three months prior to presentation, she had been definitively diagnosed with a pelvic giant cell tumor and undergone hemipelvic resection with custom prosthesis replacement. Chronic PJI developed postoperatively. Etiological examination revealed mixed infection with methicillin-resistant Staphylococcus epidermidis, extended-spectrum ß-lactamase-producing Klebsiella pneumoniae, and Pseudomonas aeruginosa. The patient underwent 8 debridement procedures with targeted antibacterial treatment. Antibacterial dosing was guided by the ratio of the area under the curve to the minimum inhibitory concentration of vancomycin plus rifampicin for biofilm penetration, together with ciprofloxacin against P. aeruginosa. The treatment strategy emphasized antibiotic rotation based on dynamic microbiome monitoring, surgical debridement with negative pressure drainage, and optimization of vancomycin trough concentration to 15-20 μg/mL via therapeutic drug monitoring. Infection did not recur during nearly 4 years of follow-up. The infection was ultimately controlled, and the prosthesis was preserved. CONCLUSIONS Patients with giant cell tumors of the pelvis who undergo prosthesis replacement should be closely monitored for PJI. Combination therapy with vancomycin and rifampicin can eradicate biofilm infections caused by coagulase-negative staphylococci, offering a potentially feasible non-revision treatment strategy for complex PJI in patients with financial constraints.},
}

Humans
Female
Adult
*Biofilms/drug effects
*Prosthesis-Related Infections/drug therapy/microbiology/therapy
*Anti-Bacterial Agents/therapeutic use
*Giant Cell Tumor of Bone/surgery
Vancomycin/therapeutic use
Debridement
*Bone Neoplasms/surgery
*Pelvic Bones/surgery
*Staphylococcal Infections/drug therapy
Pseudomonas Infections/drug therapy
Pseudomonas aeruginosa
Rifampin/therapeutic use

@article {pmid41296660,
year = {2025},
author = {Mathieu, C and Meireles, M and Pagotto, U and Wabitsch, M and Banerjee, I and Bartolomé, A and Battelino, T and Beck, J and Chiarelli, F and De Leon, DD and Dovč, K and El Goch, M and Galderisi, A and Gevers, E and Gillard, P and Haliloglu, B and Hoermann, H and Mankovsky, B and Mertens, J and Mohnike, K and Oram, R and Pasquini, T and Pearson, E and Pieber, TR and Polovina, S and Raskin, J and Roeper, M and Ruck, L and Estebanez, MS and Tankova, T and Thornton, P and van Rossum, EFC and Vukovic, R and Worth, C and Zachurzok, A},
title = {EndoCompass Project: Research Roadmap for Diabetes, Obesity, and Metabolism.},
journal = {Hormone research in paediatrics},
volume = {},
number = {},
pages = {1-31},
doi = {10.1159/000549194},
pmid = {41296660},
issn = {1663-2826},
abstract = {BACKGROUND: Endocrine science remains underrepresented in European Union research programmes despite the fundamental role of hormone health in human well-being. Analysis of the CORDIS database reveals a persistent gap between the societal impact of endocrine disorders and their research prioritization. At the national funding level, endocrine societies report limited or little attention of national research funding towards endocrinology. The EndoCompass project - a joint initiative between the European Society of Endocrinology and the European Society of Paediatric Endocrinology, aimed to identify and promote strategic research priorities in endocrine science to address critical hormone-related health challenges.

METHODS: Research priorities were established through comprehensive analysis of the EU CORDIS database covering the Horizon 2020 framework period (2014-2020). Expert consultation was conducted to identify key research priorities, followed by broader stakeholder engagement including society members and patient advocacy groups.

RESULTS: Research priorities include genetic/epigenetic factors, brain-periphery communication, and environmental influences. Key therapeutic areas include innovative approaches for monogenic disorders, incretin mimetics, dual receptor agonists, microbiome analysis, and improved behavioural interventions. For type 1 diabetes, priorities focus on early detection, insulin delivery systems, and disease-modifying therapies.

CONCLUSIONS: This component of the EndoCompass project provides an evidence-based roadmap for strategic research investment. This framework identifies crucial investigation areas into diabetes and obesity pathophysiology, prevention, and treatment strategies, ultimately aimed at reducing the burden of metabolic disorders on individuals and society. The findings support the broader EndoCompass objective of aligning research funding with areas of highest potential impact on endocrine health.},
}

@article {pmid41296394,
year = {2025},
author = {Albaijan, D and Albaijan, D and Akbar, A},
title = {Intestinal Microbial Profiles of Wild Zobaidy (Pampus argenteus) Fish Characterized by 16S rRNA Next Generation Sequencing.},
journal = {Current issues in molecular biology},
volume = {47},
number = {11},
pages = {},
doi = {10.3390/cimb47110890},
pmid = {41296394},
issn = {1467-3045},
abstract = {Pampus argenteus (Zobaidy) is an important fish in Kuwait and the Gulf region due to its economic value in the fish industry. Analyzing the gut microbiome of Zobaidy can help determine the health status of the fish and its responses to environmental changes. In this study, we investigated the microbiome composition of the intestinal tract among seven wild-caught silver pomfret specimens sampled in the Arabian gulf. The 16S rRNA was sequenced using the Illumina platform; then, sequences were analyzed using several bioinformatics tools to identify the microbial diversity, taxonomical status, and functional aspects. The results were 5933 operational taxonomic units (OTUs) categorized into 35 phyla. Proteobacteria, Firmicutes, Bacteroidota, and Actinobacterota were most abundant in the Zobaidy and water samples. At the genus level, we found high relative abundances of Acinetobacter. The results indicated that Lactococcus piscium, Enterococcus cecorum, Psychrobacter arenosus, Vagococcus salmoninarum, and Carnobacterium maltaromaticum are the most commonly present species in the analyzed Zobaidy samples. A heatmap analysis indicated notable differences in the functional categories of intestinal microflora within the Zobaidy2 sample compared to other Zobaidy samples. It should be noted that microbiome studies can provide novel ways to enhance the overall welfare of fish, strengthen disease prevention, and increase sustainability in aquaculture production.},
}

@article {pmid41296177,
year = {2025},
author = {Wang, J and Wang, B and Wang, M and Zhao, L and Liu, L and Fan, Z},
title = {Potential Benefits of Metformin Via Roseburia Intestinalis in High-fat Diet-fed Mice With Colorectal Adenomas.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41296177},
issn = {1867-1314},
support = {202110014//Nanjing Science and Technology Plan Project/ ; BE2022704//Jiangsu Science and Technology Project/ ; },
abstract = {Metformin (Met) is a pharmaceutical agent for the treatment of type 2 diabetes mellitus. Intriguingly, it may also play a role in the gastrointestinal tract, the gut microbial communities, and the tissue-resident immune cells. The present study aimed to investigate whether the administration of Met achieved protective effects on high-fat diet (HFD)-fed mice with colorectal adenomas (CRA) and elucidated its mechanism via the gut microbiota. AOM/DSS was administered in an HFD-induced diet to induce CRA in mice. 16 S rRNA sequencing was conducted to analyze the gut microbiota profile of mice. Met reduced the inflammatory response in the intestine and alleviated HFD-induced intestinal flora disturbances, and Roseburia intestinalis (R. intestinalis) colonization enhanced the efficacy of Met. Met suppressed CRA cell proliferation, which was further reduced by R. intestinalis. Met blocked NF-κB signaling by activating GILZ through increased R. intestinalis abundance. GILZ deletion in macrophages weakened the inhibition of CRA growth by Met and R. intestinalis, leading to increased macrophage M1 polarization. Inhibition of the NF-κB signaling reversed the activation of macrophage M1 polarization by knockdown of GILZ and reduced the proliferation of CRA cells. Our results shed light on the impact of Met on gut microbiome alteration in treating CRA.},
}

@article {pmid41296027,
year = {2025},
author = {Basiru, S and Legeay, J and Lee, SJ and Sani, ZK and Ziami, A and Machraoui, S and Errafii, K and Hijri, M},
title = {Phylogenetic clustering and ecological interactions of arbuscular mycorrhizal fungi and their associated microbiome of a spontaneous plant across Moroccan drylands.},
journal = {Mycorrhiza},
volume = {35},
number = {6},
pages = {68},
pmid = {41296027},
issn = {1432-1890},
support = {Project number AS-85//OCP Nutricrops/ ; },
mesh = {*Mycorrhizae/physiology/classification/genetics ; *Phylogeny ; Soil Microbiology ; *Microbiota ; Morocco ; Plant Roots/microbiology ; Ecosystem ; Rhizosphere ; Soil/chemistry ; Mycobiome ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) are ubiquitous in arid ecosystems, yet their distribution and community structure along spatial and ecological gradients remains insufficiently explored at regional scales. Here, we employed Malva sylvestris L., a native spontaneous plant species, to investigate the distribution patterns, phylogenetic structure, and community interactions of AMF and the associated root microbiome in dryland ecosystems. Sampling was conducted along a 700 km transect extending from the Atlantic coast to inland Morocco, encompassing predominantly semi-arid ecosystems. Amplicon sequencing of the LSU rDNA region of roots and soil samples revealed a highly diverse AMF assemblage spanning ten families, including Domikaceae, Diversisporaceae, Entrophosporaceae, Sclerocystaceae, and Septoglomeraceae, while the most frequent taxa belonged to the genera Dominikia, Entrophospora, Funneliformis, and Rhizophagus. Phylogenetic alpha diversity declined with increasing soil phosphorus (P) and nitrogen (N) but increased with soil potassium, precipitation, and distance from the coastline. AMF community dissimilarity in the rhizosphere was primarily explained by distance from the coastline, MAT, and precipitation together with soil P, N, whereas AMF communities in roots were mainly structured by soil P, N, and carbon. Community assembly processes among root-associated AMF were mainly shaped by total soil N and P: total N drove local AMF community structure (positive Nearest Taxon Index) while variation in soil P increased community turnover among locations (positive beta Nearest Taxon Index). Consequently, network topology was negatively correlated with soil P, and temperature, but positively with precipitation. Specialized AMF taxa, particularly Septoglomus and Funneliformis, acted as hubs in the root fungal network, whereas generalists such as Rhizophagus and Entrophospora drove cross-kingdom associations, interacting strongly with Rhizobium, Sphingomonas, and Caulobacter. Overall, this study advances our understanding of AMF ecology in dryland ecosystems and introduces an innovative bioinformatic workflow that provides new opportunities for exploring mycorrhizal diversity and functions.},
}

*Mycorrhizae/physiology/classification/genetics
*Phylogeny
Soil Microbiology
*Microbiota
Morocco
Plant Roots/microbiology
Ecosystem
Rhizosphere
Soil/chemistry
Mycobiome

@article {pmid41296011,
year = {2025},
author = {Makino, Y and Oyama, K and Sagara, A and Thege, FI and Maitra, A},
title = {Molecular pathology of intraductal papillary mucinous neoplasms of the pancreas: current understanding and perspectives on malignant progression.},
journal = {Journal of gastroenterology},
volume = {},
number = {},
pages = {},
pmid = {41296011},
issn = {1435-5922},
support = {25ck0106060h//Japan Agency for Medical Research and Development/ ; },
abstract = {Intraductal papillary mucinous neoplasms (IPMNs) of the pancreas are bona fide cystic precursor lesions to pancreatic ductal adenocarcinoma (PDAC), which is the cancer type with the most dismal prognosis. Since IPMNs are detectable by imaging, they offer a rare window of opportunity for early intervention for PDAC development. Despite their clinical visibility, the molecular pathogenesis of IPMNs remained incompletely understood, and no effective non-surgical therapeutic strategies have been established to date. In the past few decades, however, substantial progress has been made in elucidating their molecular pathology. Next-generation sequencing technologies demonstrated the comprehensive genetic mutation profile of IPMNs in the early 2010s. Elucidation of these mutation profiles enabled the establishment of genetically engineered mouse models, successfully recapitulating the natural development of human IPMNs and their progression to invasive cancer. Rapid evolution of "omics" technologies in recent years has facilitated the application of mass spectrometry, single-cell sequencing and spatial transcriptomics to IPMNs, significantly advancing our understanding of their pathophysiology. These techniques elucidated the changes in transcriptome, proteome, metabolome, microbiome, and tumor microenvironment associated with IPMN development and progression. This review summarizes current insights into the molecular and cellular landscapes of IPMN tumorigenesis, with particular emphasis on the mechanisms driving malignant progression.},
}

@article {pmid41295889,
year = {2025},
author = {Shijimaya, T and Tahara, T and Shimogama, T and Yamazaki, J and Kobayashi, S and Nakamura, N and Takahashi, Y and Tomiyama, T and Naganuma, M},
title = {Paradoxical Change in the Gastric Microbiome Structure in the Helicobacter pylori-related Advanced Gastric Mucosal Atrophy.},
journal = {Journal of clinical gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1097/MCG.0000000000002299},
pmid = {41295889},
issn = {1539-2031},
abstract = {OBJECTIVE: Risk of Helicobacter pylori (H. pylori)-related gastroduodenal diseases is influenced by the degree of chronic gastritis, while other microbes reside in gastric mucosa may be relevant to this process. This study aimed to characterize the microbiome composition in the gastric mucosa, especially with an attempt to its correlation with histologic and serological degrees of H. pylori-related gastritis.

METHODS: Among 182 cancer-free patients, bacterial communities of the gastric mucosa in the antrum were examined using 16S rRNA sequencing. The result was correlated with clinicopathological characteristics, histologic and serological degrees of H. pylori-related gastritis.

RESULTS: Bacterial alpha diversity measures were significantly lower in H. pylori clinical test positives compared with that in the negatives. Lower bacterial alpha diversity measures were also associated with degree of histologic gastritis in the antrum, while rather higher bacterial alpha diversity measures were correlated with degree of serological gastritis. The multiple regression analysis demonstrated that histologic gastritis (active gastritis, atrophy) was significantly associated with lower Shannon index (t=-4.37, P<0.0001), an indicator for bacterial alpha diversity. Inversely, serological gastritis (serum pepsinogen 3+) was also associated with higher Shannon index (t=2.98, P<0.0001). In the specific bacteria, higher abundances of Bacillus, Actinobacillus, and Streptococcus were associated with degree of serological gastritis.

CONCLUSIONS: Our findings showed paradoxical change in the microbiome structure in the development of severe gastric atrophy that may be associated with progression of gastric atrophy and gastric cancer risk.The study was not registered as the clinical trial because of the retrospective observational study.},
}

@article {pmid41295849,
year = {2025},
author = {Huo, W and Qiao, Y and He, X and Wang, C and Li, R and Che, L and Li, E},
title = {Mycotoxins and the Intestinal Epithelium: From Barrier Injury to Stem Cell Dysfunction.},
journal = {Toxins},
volume = {17},
number = {11},
pages = {},
doi = {10.3390/toxins17110534},
pmid = {41295849},
issn = {2072-6651},
mesh = {Humans ; *Mycotoxins/toxicity ; Animals ; *Intestinal Mucosa/drug effects/pathology/metabolism ; *Stem Cells/drug effects/pathology ; },
abstract = {Mycotoxins are toxic secondary metabolites produced by filamentous fungi that contaminate agricultural commodities, posing risks to food safety, animal productivity, and human health. The gastrointestinal tract is the first and most critical site of exposure, where the intestinal epithelium functions as both a physical and immunological barrier against luminal toxins and pathogens. While extensive research has demonstrated that mycotoxins disrupt epithelial integrity through tight junction impairment, oxidative stress, apoptosis, and inflammation, their effects on the intestinal stem cell (ISC) compartment and epithelial regeneration remain insufficiently understood. This review integrates recent findings from in vivo, cell culture, and advanced 3D intestinal organoid and gut-on-chip models to elucidate how mycotoxins such as deoxynivalenol and zearalenone impair ISC proliferation, alter Wnt/Notch signaling, and compromise mucosal repair. We also discuss dose relevance, species differences, and the modulatory roles of the microbiome and short-chain fatty acids, as well as emerging evidence of additive or synergistic toxicity under co-exposure conditions. By bridging well-established mechanisms of barrier disruption with the emerging concept of ISC-driven regenerative failure, this review identifies a critical knowledge gap in mycotoxin toxicology and highlights the need for integrative models that link epithelial damage to impaired regeneration. Collectively, these insights advance understanding of mycotoxin-induced intestinal dysfunction and provide a foundation for developing nutritional, microbial, and pharmacological strategies to preserve gut integrity and repair.},
}

Humans
*Mycotoxins/toxicity
Animals
*Intestinal Mucosa/drug effects/pathology/metabolism
*Stem Cells/drug effects/pathology

@article {pmid41295846,
year = {2025},
author = {Muñoz-Zavala, C and Solís-Martínez, O and Valencia-Luna, JB and Sonder, K and Hernández-Anguiano, AM and Palacios-Rojas, N},
title = {Aflatoxins in Mexican Maize Systems: From Genetic Resources to Agroecological Resilience and Co-Occurrence with Fumonisins.},
journal = {Toxins},
volume = {17},
number = {11},
pages = {},
doi = {10.3390/toxins17110531},
pmid = {41295846},
issn = {2072-6651},
support = {NA/WT_/Wellcome Trust/United Kingdom ; NA//Mexican Goverment/ ; NA//CGIAR/ ; },
mesh = {*Zea mays/microbiology/genetics ; *Fumonisins/analysis/toxicity ; *Aflatoxins/analysis/toxicity ; Mexico ; *Food Contamination/analysis ; Humans ; },
abstract = {Aflatoxins (AFs) and fumonisins (FUMs) are among the most prevalent and toxic mycotoxins affecting maize production globally. In Mexico, their co-occurrence poses a significant public health concern, as maize is not only a dietary staple but also predominantly grown and consumed at the household level. This review examines the multifactorial nature of AFs and FUMs contamination in Mexican maize systems, considering the roles of maize germplasm, agricultural practices, environmental conditions, and soil microbiota. Maize landraces, well-adapted to diverse agroecological zones, exhibit potential resistance to AFs contamination and should be prioritized in breeding programs. Sustainable agricultural practices and biocontrol strategies, including the use of atoxigenic Aspergillus flavus strains, are presented as promising interventions. Environmental factors and soil characteristics further influence fungal proliferation and mycotoxin biosynthesis. Advances in microbiome engineering, biological breeding approaches, and predictive modeling offer novel opportunities for prevention and control. The synergistic toxicity of AFs and FUMs significantly increases health risks, particularly for liver cancer, highlighting the urgency of integrated mitigation strategies. While Mexico has regulatory limits for AFs, the lack of legal thresholds for FUMs remains a critical gap in food safety legislation. This comprehensive review underscores the need for biomarker-based exposure assessments and coordinated national policies, alongside multidisciplinary strategies to reduce mycotoxin exposure and enhance food safety in maize systems.},
}

*Zea mays/microbiology/genetics
*Fumonisins/analysis/toxicity
*Aflatoxins/analysis/toxicity
Mexico
*Food Contamination/analysis
Humans

@article {pmid41295733,
year = {2025},
author = {O'Donoghue, S and Waters, SM and Morris, DW and Earley, B},
title = {A Comprehensive Review: Molecular Diagnostics and Multi-Omics Approaches to Understanding Bovine Respiratory Disease.},
journal = {Veterinary sciences},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/vetsci12111095},
pmid = {41295733},
issn = {2306-7381},
support = {16/RD/US-ROI/11//Department of Agriculture, Food and the Marine (DAFM) US-Ireland R&D partnership call/ ; 2018US-IRL200//the US- Ireland Tri Partite Grant/ ; No. 101000213//European Union Horizons 2020, HoloRuminant project/ ; },
abstract = {Bovine respiratory disease (BRD) is a multifactorial syndrome and a leading cause of morbidity and economic loss in global cattle production. Next-generation sequencing (NGS) platforms, including Illumina and Oxford Nanopore Technologies (ONT), have enabled high-resolution profiling of the bovine respiratory microbiome and virome, revealing novel viral contributors such as bovine rhinitis A virus (BRAV) and influenza D virus (IDV). Transcriptomic approaches, including RNA sequencing (RNA-Seq) and microRNA (miRNA) profiling, provide insights into host immune responses and identify potential biomarkers for disease prediction. Traditional diagnostic methods-culture, ELISA, and immunohistochemistry-are increasingly complemented by PCR-based and metagenomic techniques, improving sensitivity and specificity. Despite technological progress, gaps remain in virome characterization, miRNA function, and the integration of multi-omics data. Standardized protocols and longitudinal studies are needed to validate microbial signatures and support field-deployable diagnostics. Advances in bioinformatics, particularly network-based integrative pipelines, are becoming essential for harmonizing multi-omics datasets and revealing complex host-pathogen interactions. The objective of this comprehensive review was to synthesize current understanding of the bovine transcriptomic response to BRD as well as the respiratory microbiome and virome, emphasizing how advanced sequencing technologies have transformed microbial profiling and molecular diagnostics in BRD.},
}

@article {pmid41295688,
year = {2025},
author = {Li, Y and Wang, M and Liu, W and Geng, M and Asiri, M and Alzahrani, FM and Alzahrani, KJ and Ma, Q and Wang, C and Khan, MZ},
title = {Targeting the Gut-Mammary Axis for Understanding Mastitis Pathogenesis and Therapeutic Strategies.},
journal = {Veterinary sciences},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/vetsci12111049},
pmid = {41295688},
issn = {2306-7381},
support = {2022YFD1600103; 2023YFD1302004//National Key R&D Program of China/ ; 19211162//Livestock and Poultry Breeding Industry Project of the Ministry of Agriculture and Rural Affairs/ ; SDNYXTTG-2024-13//Shandong Province Agricultural Major Technology Collaborative Promotion Plan/ ; R.G.P.02/709/46//Deanship of Scientific Research at King Khalid University, the large research group program/ ; GDWZ202401//Liaocheng Municipal Bureau of Science and Technology, High-talented Foreign Expert Introduction Program/ ; },
abstract = {Mastitis represents one of the most economically devastating diseases in dairy production, causing billions of dollars in annual losses through reduced milk quality and quantity. Recent advances in microbiome research have unveiled a critical gut-mammary axis that fundamentally influences mastitis susceptibility and pathogenesis in dairy cattle. Through comprehensive analysis of microbial communities across multiple anatomical sites, we demonstrate that mastitis development involves systematic disruption of both mammary and gastrointestinal microbiomes, characterized by reduced beneficial bacterial populations and increased pathogenic species. Healthy animals maintain balanced microbial ecosystems dominated by protective taxa including Firmicutes, Bacteroidetes, and beneficial Lactobacillus species, while mastitis-affected animals exhibit dysbiotic shifts toward Proteobacteria dominance, elevated Streptococcus and Staphylococcus populations, and compromised microbial diversity. Mechanistic investigations reveal that gut microbiota disruption compromises systemic immune competence, alters metabolite production including short-chain fatty acids and bile acids, and influences inflammatory mediators that circulate to mammary tissue. Therapeutic interventions targeting this axis, including probiotics, prebiotics, and plant-derived compounds, demonstrate significant efficacy in restoring microbiome homeostasis and reducing mastitis severity. These findings establish the gut-mammary axis as a fundamental regulatory mechanism in mastitis pathogenesis, opening new avenues for microbiome-based prevention and treatment strategies that could significantly enhance dairy health management while addressing antimicrobial resistance concerns.},
}

@article {pmid41295659,
year = {2025},
author = {Călugărița, GA and Luca, I and Gros, RV and Căsălean, TM and Gavrilă, A and Stancu, A},
title = {Reovirus Infections in Broiler Chickens: A Narrative Review.},
journal = {Veterinary sciences},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/vetsci12111021},
pmid = {41295659},
issn = {2306-7381},
abstract = {Infections caused by avian orthoreovirus represent an emerging problem with a major impact on the global poultry industry, especially in the intensive rearing of broilers. This article addresses, in a complex manner, the etiology of some clinical syndromes of interest in poultry farming: malabsorption syndrome and arthritis/tenosynovitis syndrome. Data are presented, starting from the development and physiology of the digestive tract in broiler chickens in the post-hatch period, epidemiological data, clinical signs, morphopathological changes in the intestine, and diagnostic methods in orthoreovirus infections. The development of the digestive tract is influenced by factors such as diet, digestive enzymes, intestinal pH, and intestinal microbiome/virome. Avian orthoreoviruses, belonging to the Reoviridae family, are double-stranded RNA viruses with multiple tropism. Phylogenetic analysis revealed the existence of at least six major genotypes, with a heterogeneous geographical distribution and genetic diversity that complicates control measures with vaccination. Characterization of the intestinal virome of broilers highlights many other enteric viruses, in addition to reoviruses, with pathogenic potential in triggering malabsorption syndrome. Thus, we can state that the etiology of malabsorption syndrome is not unitary, with the association of several viruses with intestinal tropism aggravating the clinical signs. The article describes viral identification methods, including classical techniques and advanced next-generation sequencing (NGS) approaches, used to characterize the intestinal virome and emerging pathogens. Finally, for prophylaxis, autogenous vaccines adapted to local circulating strains are recommended. Frequent genetic recombinations and high antigenic variation require continuous monitoring and constant adaptation of immunization schedules to control the disease.},
}

@article {pmid41295587,
year = {2025},
author = {Arroyo, D and Peart, A and Vesely, B and Trudgian, A and Chellappah, J},
title = {Human Pathogenic Bacteria Within the Nasal and Rectal Microbiome of Macropus giganteus.},
journal = {Tropical medicine and infectious disease},
volume = {10},
number = {11},
pages = {},
doi = {10.3390/tropicalmed10110322},
pmid = {41295587},
issn = {2414-6366},
support = {xxxx//Australian Defence Force Malaria and Infectious Disease Institute, Gallipoli Barracks, Enoggera, Queensland and by the United States Department of Defense Armed Forces Health Surveillance Division-Global Emerging Infectious Disease Surveillance Branch (AF/ ; },
abstract = {This study represents the first investigation into the prevalence of pathogenic bacteria in isolated, free-ranging Eastern Grey Kangaroos (Macropus giganteus) inhabiting a human-shared environment. Samples were collected from the nasal and rectal passages of state-authorised culls of M. giganteus within a military training area, where recruits had reported recurrent cases of skin and soft tissue infections. The objective was to identify clinically relevant pathogenic microorganisms present in the nasal and rectal flora of these kangaroos. Analysis revealed carriage rates of 11% for methicillin-sensitive Staphylococcus aureus (MSSA) and 2% for methicillin-resistant S. aureus (MRSA). Other potentially pathogenic bacteria isolated included Pseudomonas spp., Streptococcus (Groups B and D), Acinetobacter spp., and multiple coagulase-negative Staphylococcus (CoNS) species. Notably, CoNS species were present in 17% of nasal isolates, with Mammaliicoccus sciuri (formerly Staphylococcus sciuri) detected in 41% of these isolates, suggesting a potential reservoir for antibiotic resistance genes and virulence factors. These findings support a One Health perspective, highlighting the interconnectedness of pathogenic bacteria, M. giganteus, humans, and their shared environment.},
}

@article {pmid41295521,
year = {2025},
author = {Mai, X and Wang, N and Zhu, C and Ma, Y and Ma, Z and Yin, L and Zhou, D},
title = {Genomic Analysis of Glycosyltransferases Responsible for Galactose-α-1,3-Galactose Epitopes in Streptococcus pneumoniae: Implications for Broadly Protective Vaccination Strategy.},
journal = {Vaccines},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/vaccines13111148},
pmid = {41295521},
issn = {2076-393X},
support = {2021YFE0200500//National Key Research and Development Plan/ ; 22120250317//Fundamental Research Funds for the Central Universities/ ; 20410713500//Shanghai Science and Technology Commission/ ; 31870972//National Natural Science Foundation of China/ ; 92359203//National Natural Science Foundation of China/ ; M0693//Sino-German Scientific Research Program/ ; },
abstract = {BACKGROUND: The origin of natural anti-galactose-α-1,3-galactose (anti-Gal) antibodies in humans is only partially understood. The gut microbiome has been proposed as an important source of galactose-α-1,3-galactose (αGal) epitopes that drive the maturation of anti-Gal-reactive B cells. Certain bacteria expressing αGal epitopes, notably Escherichia coli O86:B7, have been shown to elicit anti-Gal antibody responses in α1,3-galactosyltransferase knockout (α3GalT1 KO) mice. In this study, we investigated the interaction between currently widely used bacteria polysaccharide vaccine, the 23-valent pneumococcal polysaccharide vaccine (PPV23), which contains capsular polysaccharides (CPS) from multiple Streptococcus pneumoniae serotypes, and host anti-Gal antibodies.

METHODS: We conducted a genomic analysis to identify α1,3-galactosyltransferase (α3GalT1) genes in S. pneumoniae strains. Binding of PPV23 to anti-Gal monoclonal antibodies was evaluated by ELISA, and αGal epitope content in PPV23 was estimated using a four-parameter logistic (4PL) model fitted to the ELISA calibration data. To assess in vivo immunogenicity, we immunized α3GalT1 KO mice with PPV23 and measured serum anti-Gal IgG and IgM titers before and after vaccination.

RESULTS: Genomic analysis revealed the presence of α3GalT1 genes in S. pneumoniae strains. PPV23 showed specific binding to anti-Gal monoclonal antibodies as detected by ELISA. Quantitative modeling indicated that αGal epitopes are present at low abundance within PPV23, consistent with limited expression of αGal among a minority of included serotypes. Immunization of α3GalT1 KO mice with PPV23 induced a significant rise in anti-Gal IgG titers (mean value from 124 to 384), whereas anti-Gal IgM titers remained relatively unchanged (mean value at the range of 6500-7500). High baseline anti-Gal IgM levels observed in α3GalT1 KO mice are consistent with age-dependent induction by the gut microbiota.

CONCLUSIONS: These results provide genetic and immunological evidence that αGal epitopes derived from S. pneumoniae are present in PPV23 and can engage pre-existing anti-Gal antibodies. Our findings underscore a complex interplay among bacterial glycosyltransferase genes, vaccine polysaccharide composition, and host anti-Gal antibody repertoires, which may influence vaccine immunogenicity. Consideration of host natural antibody profiles may therefore be important for interpreting responses to carbohydrate-based vaccines and for guiding vaccine design.},
}

@article {pmid41295489,
year = {2025},
author = {Gioula, G and Exindari, M},
title = {The Gut Microbiome and Vaccination: A Comprehensive Review of Current Evidence and Future Perspectives.},
journal = {Vaccines},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/vaccines13111116},
pmid = {41295489},
issn = {2076-393X},
abstract = {The gut microbiome has emerged as a pivotal player in shaping host immune responses, with significant implications for vaccine efficacy and safety. Rather than detailing all influencing factors, this review focuses on the most critical and translational aspects of microbiome-vaccine interactions. Increasing evidence shows that the composition and functionality of the intestinal microbiota can influence both the magnitude and durability of vaccine-induced immunity. For instance, Bifidobacterium longum supplementation was shown to enhance influenza vaccine seroconversion rates by approximately 30% in clinical and preclinical models, underscoring the translational potential of microbiome modulation. Here, we provide a concise synthesis of mechanistic insights and key clinical findings that connect gut microbial composition and metabolism with vaccine outcomes. We further highlight microbiome-targeted interventions-such as probiotics, prebiotics, and postbiotics-that hold promise for optimizing vaccine responses in diverse populations. By emphasizing actionable evidence over descriptive variability, the review aims to clarify how microbiome modulation can be strategically harnessed to improve vaccine performance. Integrating microbiome modulation into vaccination strategies may enhance global immunization equity and effectiveness, offering a feasible pathway toward more durable and inclusive protection worldwide.},
}

@article {pmid41295444,
year = {2025},
author = {Tsukui, M and Yagishita, S and Tokunaga, S and Wakatsuki, S and Araki, T},
title = {Gut Microbiota Affects Mouse Social Behavior via Hippuric Acid Metabolism.},
journal = {Neurology international},
volume = {17},
number = {11},
pages = {},
doi = {10.3390/neurolint17110185},
pmid = {41295444},
issn = {2035-8385},
support = {JP23gm1010011//Japan Agency for Medical Research and Development/ ; n/a//Yakult Bio-Science Foundation (Japan)/ ; n/a//Eli Lilly (Japan)/ ; },
abstract = {BACKGROUND/OBJECTIVES: Autism spectrum disorder (ASD) is a neurodevelopmental disorder typically characterized by impaired social communication. Previous reports have postulated gut microbiota to be an important non-genetic factor affecting ASD-like phenotypes in mice, as germ-free (GF) mice show impaired social communication.

RESULTS: In this study, we identified hippuric acid (HA) as a metabolite generated via a gut microbiome-dependent mechanism that plays a role in the acquisition of social behavior during mouse development. We discovered that oral or intraperitoneal HA administration to GF mice normalizes their social behavior. Furthermore, HA administration restored oxytocin expression in the hypothalamic paraventricular nucleus and secretin expression in the subfornical organ, suggesting that HA may activate the secretin-oxytocin system to influence the social behavior of mice.

CONCLUSIONS: These findings indicate that HA may serve as an important gut microbiome-dependent mediator affecting the brain mechanisms involved in regulating social behavior.},
}

@article {pmid41295404,
year = {2025},
author = {Liu, C and Guo, Y and Gu, J and Wei, Z and Chen, P and Wang, X},
title = {The Prevalence and Diversity of Marine Toxin-Antitoxin Systems.},
journal = {Marine drugs},
volume = {23},
number = {11},
pages = {},
doi = {10.3390/md23110436},
pmid = {41295404},
issn = {1660-3397},
support = {2024YFF0507000//National Key R&D Program of China/ ; 32470032//National Science Foundation of China/ ; 92451302//National Science Foundation of China/ ; 42188102//National Science Foundation of China/ ; 2022FY100600//Science & Technology Fundamental Resources Investigation Program/ ; SCSIO2023QY03//The special fund of South China Sea Institute of Oceanology, the Chinese Academy of Sciences/ ; NA//Ocean Negative Carbon Emissions (ONCE) Program/ ; },
mesh = {*Toxin-Antitoxin Systems/genetics ; *Bacteria/genetics/metabolism ; *Aquatic Organisms/genetics ; *Marine Toxins/genetics ; Microbiota ; Seawater/microbiology ; },
abstract = {Toxin-antitoxin (TA) systems, ubiquitous in bacterial and archaeal genomes, play pivotal roles in responding to environmental stresses, forming biofilms, defending against phages, and influencing pathogen virulence. The marine environment harbors Earth's most diverse and abundant microbial communities, where microorganisms have evolved unique genetic adaptations and specialized metabolic processes to thrive amid distinct environmental challenges. Research on the presence and function of TA systems in marine bacteria lags significantly behind that in model bacteria and pathogens. Here, we explored the diversity of the TA system in marine bacteria, including species from the Global Ocean Microbiome Catalogue (GOMC) and the Mariana Trench Environment and Ecology Research (MEER) databases. Our findings revealed that types I to VII (featuring protein toxins) of eight types of TA systems are prevalent in these microorganisms, with unidentified TA combinations diverging from previously characterized systems. Interestingly, some toxins or antitoxins lack canonical counterparts, indicating evolutionary divergence. Additionally, previously uncharacterized potential TA systems have been identified in extremophilic bacteria from the deep-sea Mariana Trench. These results highlight the adaptive importance of marine TA systems, which are likely operating through unconventional mechanisms.},
}

*Toxin-Antitoxin Systems/genetics
*Bacteria/genetics/metabolism
*Aquatic Organisms/genetics
*Marine Toxins/genetics
Microbiota
Seawater/microbiology

@article {pmid41295311,
year = {2025},
author = {Mori, A and Kuboniwa, M and Fukusaki, E},
title = {Comprehensive GC/MS Profiling of Volatile Organic Compounds in Whole and Glandular Saliva Using MonoTrap Micro-Extraction.},
journal = {Metabolites},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/metabo15110726},
pmid = {41295311},
issn = {2218-1989},
support = {JP 24K01271//Japan Society for the Promotion of Science/ ; },
abstract = {BACKGROUND/OBJECTIVES: Salivary volatile organic compounds (VOCs) are promising noninvasive biomarkers for a wide range of diseases. While glandular saliva, secreted by salivary glands, is a relatively pure biofluid, whole saliva is a complex mixture containing oral microbiota, food debris, and desquamated epithelial cells. Therefore, a comprehensive comparison of the VOC profiles of these two types of saliva is essential to identify biologically relevant compounds. In this study, we aimed to establish a reliable method for VOC profiling from small saliva volumes and identify VOCs that reflect the biological differences between glandular and whole saliva.

METHODS: We developed a protocol combining MonoTrap extraction with dichloromethane, allowing the analysis of VOCs from just 100 µL of saliva. To address the issue of sampling-derived artifacts, we implemented a two-step blank analysis to systematically exclude compounds originating from the collection device.

RESULTS: Our analysis successfully identified a total of 72 VOCs. Following blank analysis, we systematically excluded 15 artifacts originating from the sampling device. Subsequent orthogonal partial least squares discriminant analysis (OPLS-DA) and Wilcoxon signed-rank test (using variable importance for prediction (VIP) > 1.0 and q < 0.05) identified 10 key VOCs that were significantly higher in whole saliva than in glandular saliva. These compounds included isobutyric acid, isovaleric acid, 4-methylvaleric acid, 3-phenylpropionic acid, indole, skatole, methyl mercaptan, 1-propanol, δ-valerolactam, and acetaldehyde. Most of these compounds originate from the metabolic activities of the oral microbiome, suggesting that the distinct VOC profile of whole saliva is predominantly influenced by microbial activity.

CONCLUSIONS: Our findings demonstrated the effectiveness of this method for identifying biologically relevant VOCs from relatively small sample volumes. The identified VOC profiles highlight the contribution to the discovery of non-invasive biomarkers for oral health and serve as a solid foundation for future research into clinical applications.},
}

@article {pmid41295298,
year = {2025},
author = {Chang, T and Xue, Y and Liu, F and Zheng, R and Zhang, Z and Zheng, Q and Wang, P},
title = {Multi-Omics Decoding of Potential Microbial-Genetic Synergy Underlying Polysaccharide and Glycosidic Polymer Biosynthesis in Two Cultivars of Lilium brownii var. viridulum Baker.},
journal = {Metabolites},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/metabo15110712},
pmid = {41295298},
issn = {2218-1989},
support = {the Youth Fund of Natural Science Foundation of Hunan Province(2024JJ6332)//Putao Wang/ ; Excellent Young Project of the Education Department of Hunan Province (24B1087)//Putao Wang/ ; Excellent Young Project of the Education Department of Hunan Province (24B1085)//Fan Liu/ ; Research Program of Chinese Medicine of Hunan Province (A2023004)//Qinfang Zheng/ ; },
abstract = {Background: The accumulation of glycosidic polymers in Lilium brownii var. viridulum Baker (Lv) bulbs fundamentally governs the nutritional and medicinal properties. Methods: In this study, metabolomic, transcriptomic, and microbiome analyses were integrated to elucidate the differential mechanisms of glycoside accumulation between the elite 'Xuefeng' (Lv, X) and 'Longya' (Lv, L), each comprising three biological replicates. Results: The results demonstrate significantly elevated diversity and abundance of glycosides in X bulbs, with glucose derivatives constituting the predominant fraction. Differential expression genes (DEGs) associated with carbohydrate metabolism were primarily enriched in starch/sucrose metabolism and amino sugar metabolic pathways. Planctomycetes in rhizospheric soil, combined with Acidobacteriia and Rhodanobacteraceae in non-rhizospheric soil, were identified as key microbial taxa associated with glycoside accumulation. Variation partitioning analysis (VPA) revealed that synergistic genetic microbiota-host interactions collectively accounted for 86.8% of the metabolic variance. Conclusions: Consequently, X exhibits superior potential as a medicinal/edible cultivar and as a breeding material due to its enhanced biosynthesis of glycosidic polymers. This work, for the first time, systematically deciphers the regulatory framework of glycoside accumulation in Lv bulbs, highlighting microbiota-host synergy, and provides critical insights for the refining of biosynthetic pathways and targeted crop enhancement.},
}

@article {pmid41295294,
year = {2025},
author = {Ma, Y and Li, J and Yuan, X and Tao, W and Zhou, W and Xing, J and Yang, Y and Zhang, H},
title = {Dendrobium officinale Polysaccharide Relieves the DSS-Induced Chronic Colitis in C57BL/6J Mice and Regulates Colonic Microflora Structure.},
journal = {Metabolites},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/metabo15110708},
pmid = {41295294},
issn = {2218-1989},
support = {2024Z281//Science & Technology Innovation Program of Yongjiang 2035/ ; },
abstract = {Background/Objectives: Chronic colitis presents a growing global health burden with rising incidence. This study investigated the ameliorative effect of Dendrobium officinale polysaccharide (DOP) against dextran sulfate sodium (DSS)-induced chronic colitis in mice, specifically examining its dual modulation of gut microbiota and metabolic pathways. Methods: DOP was extracted and purified from Dendrobium officinale stems and leaves. A chronic colitis model was established in male C57BL/6J mice via DSS induction. Eighty-four mice were randomized into seven groups: control, model, low/high-dose leaf-DOP, low/high-dose stem-DOP, and sulfasalazine positive control. We assessed body weight, disease activity index (DAI), colon length, splenic/thymic indices, inflammatory cytokines, and histopathology (Hematoxylin and Eosin/Alcian blue staining), with tight junction protein and tumor necrosis factor-alpha (TNF-α) expression quantified via immunofluorescence. 16S rRNA sequencing and untargeted metabolomics evaluated microbial and metabolic shifts. Results: DOP significantly attenuated colitis severity, restored colon histoarchitecture, elevated goblet cell counts, upregulated zonula occludens-1 (ZO-1) and occludin expression, and suppressed TNF-α. Crucially, DOP remodeled dysbiosis by enriching beneficial taxa (e.g., Candidatus_Saccharimonas, Lachnoclostridium) while reducing pathogens (Mucispirillum). Metabolomics further elucidated DOP-mediated regulation of purine and nicotinate/nicotinamide metabolism-pathways mechanistically linked to its anti-inflammatory and barrier-repair effects. Conclusions: DOP effectively alleviates symptoms of DSS-induced chronic colitis in mice, protects intestinal barrier integrity, and achieves therapeutic potential through simultaneous regulation of the gut microbiome and metabolome.},
}

@article {pmid41295278,
year = {2025},
author = {Shehata, F and Dwyer, KM and Axtens, M and McGee, SL and Rivera, LR},
title = {Impact of a Lifestyle Intervention on Gut Microbiome Composition: A Quasi-Controlled Before-and-After Analysis.},
journal = {Metabolites},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/metabo15110692},
pmid = {41295278},
issn = {2218-1989},
abstract = {Background: The human gastrointestinal tract harbors a complex microbiota that plays a vital role in metabolic health. Dysbiosis of the gut microbiome has been linked to metabolic syndrome (MetS), a growing health concern characterized by obesity, hypertension, and dyslipidemia, all of which are strongly associated with insulin resistance and low-grade inflammation. This study aimed to analyze changes in gut microbiome composition and metabolic parameters in individuals with MetS following a 3-month shared medical appointment program driven by a patient-centered agenda with an emphasis on lifestyle pillars of diet, activity, sleep, and stress management. Methods: Thirty-six individuals with MetS were recruited. Of these, 14 completed a structured metabolic health program with facilitated group appointments, including personalized dietary adjustments, increased physical activity, stress management, and clinical monitoring, while 22 served as an untreated group. Fecal samples were collected for full-length 16S rRNA sequencing. Clinical and biochemical parameters, including body weight, blood pressure, HbA1c, triglycerides, and liver enzymes, were assessed. Microbiome data were analyzed for alpha and beta diversity and differential abundance. Correlations between microbial genera and clinical parameters were evaluated using Spearman correlation. Results: Post-intervention, significant improvements were observed in body weight (p = 0.0061), HbA1c (p = 0.033), triglycerides (p = 0.047), AST (p = 0.016), and systolic blood pressure (p = 0.020). Alpha and beta diversity of the gut microbiome showed no significant changes. However, differential abundance analysis revealed increased levels of butyrate-producing and anti-inflammatory genera including Duncaniella, Megasphaera, Pseudoruminococcus, and Oliverpabstia. Conclusions: A 3-month lifestyle intervention in individuals with MetS was associated with marked improvements in metabolic health and beneficial shifts in gut microbiota composition. These findings suggest that even small lifestyle modifications may be a potential therapeutic target for metabolic syndrome management, highlighting the need for personalized approaches in future research.},
}

@article {pmid41295272,
year = {2025},
author = {Bilani, N and Charbel, N and Rizkallah, J and Sater, S and Kreidieh, F},
title = {New Frontier in Cancer Immunotherapy: Sexual Dimorphism of Immune Response.},
journal = {Metabolites},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/metabo15110686},
pmid = {41295272},
issn = {2218-1989},
abstract = {Sexual dimorphism influences immune responses, cancer progression, and therapeutic outcomes, yet its metabolic underpinnings remain underexplored. Metabolomics enables the comprehensive profiling of biochemical pathways that shape sex-based differences in immune function and immunotherapy efficacy. Meta-analytic data indicate that men achieve a larger overall survival benefit from immune checkpoint inhibitors than women (pooled hazard ratio 0.72, 95% CI 0.65-0.79 vs. 0.86, 95% CI 0.79-0.93), while women may experience higher major pathologic response rates in neoadjuvant settings. At the biomarker level, elevated kynurenine-to-tryptophan ratios-reflecting indoleamine 2,3-dioxygenase activity-and distinct lipidomic signatures associate with reduced immunotherapy efficacy and may vary by sex. Sex-specific differences in microbiome-derived metabolites, including short-chain fatty acids, further modulate systemic immunity and treatment response. Ongoing clinical investigations combine hormone modulation with immune checkpoint blockade and increasingly integrate metabolomic profiling to identify predictors of benefit and toxicity. This review will synthesize meta-analytic and mechanistic evidence on sex differences in immunotherapy outcomes, highlight metabolomic biomarkers linked to response, and summarize ongoing clinical trials that incorporate metabolomics to guide sex-aware precision oncology. Understanding sex-specific metabolic pathways can refine patient stratification and optimize immunotherapeutic strategies.},
}

@article {pmid41295270,
year = {2025},
author = {Kovacs, ED and Kovacs, MH},
title = {Land Use Shapes the Rhizosphere Microbiome and Metabolome of Naturally Growing Barbarea vulgaris.},
journal = {Metabolites},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/metabo15110684},
pmid = {41295270},
issn = {2218-1989},
support = {Grant number 760104/23 May 2023, code CF 245/29, November 2022. This work was supported by the project "Sensing, Mapping, Interconnecting: Tools for soil functions and services evaluation"//European Union NextGeneration EU through the National Recovery and Resilience Plan, Component 9. I8. and Romanian Government, Ministry of the Innovation and Digitization through the National Recovery and Resilience Plan (PNRR) PNRR-III-C9-2022-I8, contrac/ ; },
abstract = {Background: Land use change fundamentally alters soil microbial communities and biochemical processes, yet the integrated effects on rhizosphere microbiome-metabolome networks remained poorly understood. Objective: This study investigated land uses as forest, grassland and intermediary edge shape the rhizosphere biochemical networks of naturally grown Barbarea vulgaris. Methods: Rhizosphere soils of Barbarea vulgaris were analysed for microbial community structure abundance, and metabolomic profile applying phospholipid fatty acid (PLFA) profiling and mass spectrometric untargeted metabolomics (GC-MS/MS and MALDI-TOF/TOF MS). These were coupled with co-inertia analysis to assess microbiome-metabolome interactions. Results: Microbial community analysis revealed significant effects of land use on bacterial community structure (G+/G-, p < 0.001). Untargeted metabolomics identified 248 metabolites, of which 161 were mapped to KEGG pathways. Amino acids and derivatives (21.1%) followed by organic acids (16.8%) were the most representative among identified metabolites. Pathway enrichment analysis revealed coordinated reprogramming of central carbon and nitrogen metabolism across land use gradients, particularly in the amino acid metabolism, TCA cycle, and glycolysis/gluconeogenesis pathways. Microbiome-metabolome coupling analysis revealed distinct correlation patterns between microbial phenotypes and metabolite classes, with forest environments showing the strongest biochemical network integration (RV = 0.91). Edge habitats presented intermediate signatures, supporting their role as transitional zones with unique biochemical properties. Conclusions: The environmental context fundamentally shapes rhizosphere biochemical network organization through coordinated shifts in bacterial community structure and metabolic pathway activity. These habitat-specific metabolic signatures suggest that land use change triggers adaptive biochemical responses that may influence plant performance and ecosystem functioning across environmental gradients.},
}

@article {pmid41295254,
year = {2025},
author = {Lauricella, S and Brucchi, F and Cirocchi, R and Cassini, D and Vitellaro, M},
title = {The Gut Microbiome in Early-Onset Colorectal Cancer: Distinct Signatures, Targeted Prevention and Therapeutic Strategies.},
journal = {Journal of personalized medicine},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/jpm15110552},
pmid = {41295254},
issn = {2075-4426},
abstract = {Background/Objectives: The incidence of early-onset colorectal cancer (EOCRC) is rising worldwide, although its biological and clinical features remain incompletely understood. Emerging evidence implicates gut microbial dysbiosis as a key driver of EOCRC pathogenesis, acting through complex interactions with host genetics, mucosal immunity, and early-life exposures. This review synthesizes current evidence on EOCRC-specific microbial signatures, delineates host-microbiome interactions, and evaluates how these insights may inform precision prevention, early detection, and therapeutic strategies. Methods: A systematic literature search was conducted in PubMed, Scopus, and Web of Science up to August 2025, using combinations of "early-onset colorectal cancer," "gut microbiome," "dysbiosis," and "host-microbiome interactions." Both clinical and preclinical studies were included. Extracted data encompassed microbial composition, mechanistic insights, host-related factors, and microbiome-targeted interventions. Evidence was synthesized narratively to highlight consistent patterns, methodological limitations, and translational implications. Results: EOCRC is consistently associated with enrichment of pro-inflammatory and genotoxic taxa (e.g., Fusobacterium nucleatum, colibactin-producing Escherichia coli, enterotoxigenic Bacteroides fragilis) and depletion of short-chain fatty acid-producing commensals. Multi-omics analyses reveal distinct host-microbiome signatures influenced by germline predisposition, mucosal immunity, sex, and early-life exposures. However, substantial methodological heterogeneity persists. Collectively, these data point to candidate microbial biomarkers for early detection and support the rationale for microbiome-targeted preventive and adjunctive therapeutic approaches. Conclusions: EOCRC harbors unique microbial and host-environmental features that distinguish it from late-onset disease. Integrating host determinants with microbiome signatures provides a framework for precision prevention and tailored therapeutic strategies. Future priorities include harmonizing methodologies, validating microbial biomarkers in asymptomatic young adults, and rigorously testing microbiome-targeted interventions in clinical trials.},
}

@article {pmid41295186,
year = {2025},
author = {Grando, D and Watson, CJ},
title = {Perspectives on Vaginal Ecology and Management of Recurrent Vulvovaginal Candidiasis: A Narrative Review.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/jof11110806},
pmid = {41295186},
issn = {2309-608X},
abstract = {Symptomatic vulvovaginal candidiasis (VVC) affects around three-quarters of women at least once in their lifetime. Around 10% of these women will experience prolonged or recurrent vulvovaginal candidiasis (RVVC), which fails to respond, despite following recommended therapy. Most commonly prescribed therapy involves suppression therapy-usually for two weeks-which aims at eliminating symptoms by frequent administration of antifungals, followed by maintenance (weekly/monthly) therapy for up to six months. However, following cessation of maintenance therapy, around 50% of these women experience relapse. The vaginal ecology of RVVC can be characterized, and it is thought that biofilms and/or the development of antifungal resistance prevent adequate resolution. However, hypersensitivity may also confound management. This narrative review was performed to identify key studies that examine the management of VVC and the challenges of current prolonged antifungal therapy. It identifies gaps that show it remains important to investigate microbiological findings in RVVC and how these may inform rational choices in therapy in an era of rising antimicrobial resistance. Hope exists, as studies of the vaginal microbiome highlight that the type of microbiota may influence the level of inflammation and reduce symptomatology. Future research will continue to explore whether a personalized medicine approach can promote healthy vaginal ecology and prevent the debilitating long-term effects of RVVC.},
}

@article {pmid41295160,
year = {2025},
author = {Wright, E and Valand, N and Venkatraman Girija, U},
title = {Harnessing Probiotics to Combat Candidiasis: Mechanisms, Evidence, and Future Directions.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/jof11110779},
pmid = {41295160},
issn = {2309-608X},
abstract = {Candida species are common commensals within the human microbiome but can transition opportunistically to pathogenic states when host-microbe homeostasis is disrupted. Their ability to adhere to mucosa and implanted medical devices, form thick biofilms, and invade epithelial tissues makes candidiasis particularly harmful in immunocompromised and elderly populations. This review examines the reported antifungal activity of common probiotic genera such as Lactobacillus, Bacillus, Bifidobacterium, and Saccharomyces across the oral cavity, gastrointestinal tract, and vaginal tract. The probiotic mechanisms of action, such as competitive exclusion, secretion of antifungal metabolites, and immunomodulation, are explored in detail, and research methodologies are scrutinised to assess the robustness of current evidence. This review compiles evidence from a variety of studies and clinical trials showing certain probiotic strains and formulations have the ability to significantly decrease Candida colonisation and reduce candidiasis symptom prevalence. Although outcomes vary greatly between probiotic strains tested, species of Candida targeted, and specific site of infection, it is clear that selected probiotic species and their secreted substances can have prominent anti-Candida effects and promote tangible clinical improvements. Future directions for the field of probiotic study are suggested, including the roles of prebiotics, postbiotics, and synbiotic formulations to enhance probiotic efficacy against candidiasis.},
}

@article {pmid41295149,
year = {2025},
author = {Zeng, Y and Wang, Y and Wang, X and Jing, X and Shu, X and Ren, P and Liu, W and Ye, Q and Fu, W and Hao, Z and Zhang, X and Chen, B and Wang, X},
title = {Arbuscular Mycorrhizal Fungi as Core Engineers in Synthetic Microbial Communities: Boosting Plant Growth and Soil Health for Sustainable Agriculture.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/jof11110769},
pmid = {41295149},
issn = {2309-608X},
support = {2023YFF1306004//the National Key Research and Development Program of China/ ; 2024NSFSC0860//Sichuan Science and Technology Program/ ; 42207050//National Natural Science Foundation of China grant/ ; 42377299//National Natural Science Foundation of China grant/ ; 42177109//National Natural Science Foundation of China grant/ ; 2023NSFSC1979//Sichuan Science and Technology Program/ ; },
abstract = {Bacterial synthetic microbial communities (SynCom) have exhibited significant effects for enhancing plant growth and delivering ecological benefits. However, persistent challenges, including structural instability, limited environmental adaptability, and transient efficacy, remain critical barriers to their practical application. Herein, we propose Arbuscular Mycorrhizal fungi (AMF) as the keystone component to optimize SynCom's ecological fitness in sustainable agricultural systems. AMF modulate microbiome assembly through hyphal networks, enhancing community stability via facilitative interactions and augmenting nutrient cycling functionalities. This review systematically evaluates methodologies for AMF-based SynCom design and construction, investigates the dynamics of AMF-microbe interactions, delineates plant growth-promoting mechanisms, identifies candidate microbial taxa, and addresses implementation bottlenecks with corresponding strategies. We posit that AMF-Based SynComs represent a transformative management tool for ensuring global food security amid impending climatic perturbations and declining agricultural productivity.},
}

@article {pmid41294874,
year = {2025},
author = {Paciolla, C and Manganelli, M and Di Chiano, M and Montenegro, F and Gallone, A and Sallustio, F and Guida, G},
title = {Valeric Acid: A Gut-Derived Metabolite as a Potential Epigenetic Modulator of Neuroinflammation in the Gut-Brain Axis.},
journal = {Cells},
volume = {14},
number = {22},
pages = {},
doi = {10.3390/cells14221823},
pmid = {41294874},
issn = {2073-4409},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Epigenesis, Genetic/drug effects ; *Neuroinflammatory Diseases/genetics/metabolism/drug therapy ; Animals ; *Brain/metabolism/drug effects ; *Pentanoic Acids/metabolism/pharmacology ; Histone Deacetylase Inhibitors/pharmacology ; *Brain-Gut Axis ; },
abstract = {The gut-brain axis (GBA) is a critical area of research for understanding the pathogenesis of neuroinflammatory and neurodegenerative diseases. Metabolites produced by the gut microbiota, particularly short-chain fatty acids (SCFAs), act as key mediators in this bidirectional communication. While the roles of acetate, propionate, and butyrate are well-established, valeric acid (VA), a five-carbon SCFA, is poorly understood. This comprehensive review explores VA as a gut-derived physiological epigenetic modulator, examining its microbial biosynthesis and systemic effects. This review discusses how VA acts as a selective histone deacetylase inhibitor (HDACi), particularly targeting Class I HDACs, to modulate gene expression and exert neuroprotective and anti-inflammatory effects. The analysis compares VA with its pharmacological analog, valproic acid (VPA), a well-known but non-selective HDACi. This comparison highlights how VA's physiological nature may offer a more targeted and safer intervention. In conclusion, elucidating VA's role as a microbiome-derived epigenetic regulator would open promising avenues for therapeutic strategies that directly connect gut and CNS health within the GBA.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Epigenesis, Genetic/drug effects
*Neuroinflammatory Diseases/genetics/metabolism/drug therapy
Animals
*Brain/metabolism/drug effects
*Pentanoic Acids/metabolism/pharmacology
Histone Deacetylase Inhibitors/pharmacology
*Brain-Gut Axis

@article {pmid41294866,
year = {2025},
author = {Blanco, JR and Del Campo, R and Avendaño-Ortiz, J and Laguna-Olmos, M and Carnero, A},
title = {The Role of Microbiota in Ovarian Cancer: Implications for Treatment Response and Therapeutic Strategies.},
journal = {Cells},
volume = {14},
number = {22},
pages = {},
doi = {10.3390/cells14221813},
pmid = {41294866},
issn = {2073-4409},
mesh = {Humans ; Female ; Animals ; *Ovarian Neoplasms/microbiology/therapy ; *Microbiota ; Dysbiosis/microbiology ; Gastrointestinal Microbiome ; },
abstract = {Cancer remains a global health challenge (18.1 million new cases in 2020), with incidence projected to reach 28 million within two decades. Ovarian cancer (OC) is the deadliest gynecologic malignancy, usually diagnosed at advanced stages and with poorly understood etiology. Emerging evidence implicates reproductive tract and gut microbiota in OC biology. Microbiota shape carcinogenesis via turnover, immunity, and metabolism; dysbiosis promotes DNA damage, inflammation, and carcinogenic metabolites, engaging multiple hallmarks of cancer. In OC, microbes may reach tumors by local ascent, translocation, or hematogenous spread, originating from vagina, upper reproductive tract, peritoneal fluid, or gut. Lactobacillus-dominant vaginal communities support mucosal integrity, whereas anaerobes disrupt barriers, increase inflammation, and correlate with OC risk; mouse models show vaginal dysbiosis accelerates tumor progression. Distinct microbial profiles in upper reproductive sites and peritoneal fluid associated with immune remodeling. Gut dysbiosis drives barrier loss, immune imbalance, and estrogen reactivation. Microbial metabolites (lipopolysaccharides, short-chain fatty acids) modulate oncogenic pathways, altering epithelial-mesenchymal transition, immune evasion, and drug resistance. Across cohorts, OC tissues and fluids show Pseudomonadota/Bacteroidota enrichment and Akkermansia depletion; fecal microbiota from OC patients accelerates tumor growth in mice, whereas Akkermansia supplementation restores antitumor immunity. Antibiotic exposure and platinum resistance associate with reduced diversity and expansion of lactate-producing taxa. Microbiome-informed interventions-diet, probiotics/postbiotics, fecal microbiota transfer, and selective antibiotics-may augment chemotherapy and immunotherapy. Overall, the microbiome is a modifiable determinant of OC risk, progression, and treatment response, warranting rigorous, standardized, multi-omics studies.},
}

Humans
Female
Animals
*Ovarian Neoplasms/microbiology/therapy
*Microbiota
Dysbiosis/microbiology
Gastrointestinal Microbiome

@article {pmid41294832,
year = {2025},
author = {Susiriwatananont, T and Eiamprapaporn, P and Vazquez Roque, M and Farraye, FA and Perlman, A and Chumsri, S},
title = {The Gut Microbiome as a Biomarker and Therapeutic Target of Immune Checkpoint Inhibitors: A Review for Oncologists.},
journal = {Cells},
volume = {14},
number = {22},
pages = {},
doi = {10.3390/cells14221779},
pmid = {41294832},
issn = {2073-4409},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/immunology ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Oncologists ; *Neoplasms/drug therapy/immunology/microbiology ; Biomarkers/metabolism ; Immunotherapy/methods ; Biomarkers, Tumor/metabolism ; Animals ; Fecal Microbiota Transplantation ; },
abstract = {Immune checkpoint inhibitors (ICIs) have transformed cancer therapy, yet their benefits remain limited to a subset of patients, underscoring the need for more reliable biomarkers and novel therapeutic strategies. The gut microbiome has emerged as a critical modulator of systemic immunity and a promising determinant of ICI response. Evidence links specific microbial features, taxa, and bioactive metabolites to enhanced antitumor immunity, whereas disruptions, such as antibiotic exposure, are associated with poorer outcomes. Advances in sequencing and multi-omics technologies have provided more profound insights into microbiome-immune crosstalk, though methodological heterogeneity continues to challenge reproducibility. Translational studies demonstrate that microbiome-based intervention, including fecal microbiota transplantation (FMT), biotics supplementation, and engineered microbial strains, can enhance ICI efficacy or mitigate immune-related toxicities. Despite encouraging early clinical signals, broader implementation requires methodological rigor, standardized protocols, and innovative trial designs that account for host and environmental factors. For clinicians, the most immediate strategies involve prudent antibiotic stewardship and patient enrollment in microbiome-focused clinical trials. Overall, the gut microbiome is a promising biomarker and a therapeutic target, representing a new frontier for personalizing immunotherapy and improving patient outcomes in oncology.},
}

Humans
*Gastrointestinal Microbiome/drug effects/immunology
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
*Oncologists
*Neoplasms/drug therapy/immunology/microbiology
Biomarkers/metabolism
Immunotherapy/methods
Biomarkers, Tumor/metabolism
Animals
Fecal Microbiota Transplantation

@article {pmid41294692,
year = {2025},
author = {Wang, YS and Wang, QY and Moise, AE and Syed, HC and Malo, J and Soberano, S and Belkaid, W and Messaoudene, M and Bélanger, K and Desilets, A and Jamal, R and Routy, B and Elkrief, A},
title = {Antibiotic Exposure Does Not Impact Anti-BRAF/Anti-MEK Targeted Therapy Outcome in Patients with Advanced Melanoma.},
journal = {Current oncology (Toronto, Ont.)},
volume = {32},
number = {11},
pages = {},
doi = {10.3390/curroncol32110630},
pmid = {41294692},
issn = {1718-7729},
support = {Not applicable//Seerave Foundation/ ; },
mesh = {Humans ; *Melanoma/drug therapy/pathology ; Male ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Female ; Middle Aged ; *Proto-Oncogene Proteins B-raf/antagonists & inhibitors/genetics ; Aged ; Retrospective Studies ; Adult ; Treatment Outcome ; *Protein Kinase Inhibitors/therapeutic use/pharmacology ; Immune Checkpoint Inhibitors/therapeutic use ; Aged, 80 and over ; },
abstract = {The gut microbiome is an established predictor of response to immune checkpoint inhibitors (ICI) in melanoma, and antibiotic exposure prior to ICI initiation is a validated negative prognostic factor. About half of melanoma patients harbor BRAF mutations and are treated with BRAF/MEK inhibitors (BRAFi/MEKi). While the detrimental impact of antibiotics is well described in the ICI setting, their effect on BRAFi/MEKi efficacy remains unknown. We retrospectively analyzed 49 advanced BRAF-mutant melanoma patients treated with BRAFi/MEKi. Antibiotic-exposed patients were compared with non-exposed patients across three time windows: within 30, 60, or 90 days before and after therapy initiation. Outcomes included progression-free survival (PFS), overall survival (OS), and overall response rate (ORR). Among the cohort, 41% had antibiotic exposure within ±30 days, 53% within ±60 days, and 57% within ±90 days. Baseline characteristics were comparable between groups, except for worse ECOG scores in antibiotic-exposed patients. Across all windows, ORR, PFS, and OS were comparable between groups. Unlike what was observed in the ICI setting, antibiotic use did not negatively affect outcomes with BRAFi/MEKi. Despite small sample size, these findings suggest that the detrimental prognostic impact of antibiotics is specific to immunotherapy, highlighting the importance of evaluating the microbiome as a predictive biomarker across treatment contexts.},
}

Humans
*Melanoma/drug therapy/pathology
Male
*Anti-Bacterial Agents/therapeutic use/pharmacology
Female
Middle Aged
*Proto-Oncogene Proteins B-raf/antagonists & inhibitors/genetics
Aged
Retrospective Studies
Adult
Treatment Outcome
*Protein Kinase Inhibitors/therapeutic use/pharmacology
Immune Checkpoint Inhibitors/therapeutic use
Aged, 80 and over

@article {pmid41294637,
year = {2025},
author = {Ionaș, TH and Ionaș, M and Chicea, R and Dădârlat, DA and Ștef, L},
title = {Assessing the Oral Microbiome in Women of Reproductive Age: A Narrative Review.},
journal = {Clinics and practice},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/clinpract15110206},
pmid = {41294637},
issn = {2039-7275},
abstract = {The oral microbiome may be an indicator of oral pathologies and hormonal fluctuations. Consequently, the proper identification of methods for studying microbial factors is essential. Because more than half of the components of the oral microbiome belong to species that are very difficult or even impossible to cultivate in the laboratory, the assessment of the oral microbiome nowadays is based on genetic sequencing, using techniques such as DNA hybridization, 16S rRNA sequencing, and metagenomics, mainly analyzing saliva and subgingival plaque. Variations in results may be caused by differences in sample type, analysis methods, accuracy in determining cycle phases, and biases introduced by DNA extraction techniques and technical variations. Choosing the right primers for the 16S rRNA gene and reference databases (like HOMD, Greengenes2) is essential for accurately identifying microorganisms. Metagenomic sequencing offers greater taxonomic and functional detail, but it is costlier and presents bioinformatics challenges, including contamination with human DNA. When the patients under study are women, we have to take into consideration the cyclical changes in the menstrual cycle. Studies suggest that estrogen influences local immune and inflammatory responses and can worsen existing gingival inflammation. Certain oral bacteria can even utilize estradiol and progesterone as growth factors. The composition of the oral microbiome is also affected by hormonal contraceptives, carbohydrate intake, smoking, age, body mass index, genetics, and oral hygiene-all factors that need to be controlled for in future studies. Interpreting the biological significance of the reported cyclic changes requires careful examination of the specific methods used in each study.},
}

@article {pmid41294522,
year = {2025},
author = {Špiljak, B and Andabak Rogulj, A and Lončar Brzak, B and Brailo, V and Škrinjar, I and Ozretić, P and Vidović Juras, D},
title = {Desquamative Gingivitis and the Oral Microbiome: Insights into Immune-Microbial Interactions in Mucosal Inflammation.},
journal = {Dentistry journal},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/dj13110541},
pmid = {41294522},
issn = {2304-6767},
abstract = {Desquamative gingivitis (DG) is a clinical presentation characterized by erythema, epithelial desquamation, and mucosal fragility, commonly associated with immune-mediated diseases such as oral lichen planus (OLP), mucous membrane pemphigoid (MMP), and pemphigus vulgaris (PV). While traditionally viewed as a manifestation of immune dysregulation, growing evidence suggests that the oral microbiome may modulate disease onset, persistence, and severity. This review summarizes current knowledge on the oral microbiota in DG and its underlying diseases, explores mechanistic links between dysbiosis and immune activation, and discusses clinical and research implications. A narrative literature review was conducted using PubMed and Scopus, focusing on studies analyzing the oral microbiome in OLP, MMP, and PV. Emphasis was placed on molecular microbiology techniques, immune profiling, and functional or longitudinal approaches. In OLP, microbial dysbiosis is consistently reported, including reduced diversity and increased abundance of pro-inflammatory genera such as Fusobacterium, Prevotella, and Capnocytophaga. These shifts correlate with epithelial barrier disruption and inflammatory cytokine production. Although data on MMP and PV are limited, early findings suggest microbial involvement in sustaining inflammation, delaying healing, and possibly amplifying autoimmune responses. Dysbiosis may activate Toll-like receptors, skew T cell responses, and contribute to the breakdown of immune tolerance. DG may reflect a dynamic interplay between immune mechanisms and microbial ecology. While evidence is strongest for OLP, preliminary data suggest broader microbial contributions across DG-associated diseases. Microbiome-informed approaches could enhance diagnostic accuracy and support the development of adjunctive therapies.},
}

@article {pmid41294484,
year = {2025},
author = {Dioguardi, M and Lo Muzio, E and Guerra, C and Sovereto, D and Laneve, E and Martella, A and Aiuto, R and Garcovich, D and Caloro, GA and Cantore, S and Lo Muzio, L and Ballini, A},
title = {Liver Disease and Periodontal Pathogens: A Bidirectional Relationship Between Liver and Oral Microbiota.},
journal = {Dentistry journal},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/dj13110503},
pmid = {41294484},
issn = {2304-6767},
support = {PE_00000019//European Union/ ; },
abstract = {Background: Periodontal dysbiosis contributes to liver injury through systemic inflammation, oral-gut microbial translocation, and endotoxemia. Lipopolysaccharides (LPSs) and virulence factors derived from periodontal pathogens, particularly Porphyromonas gingivalis (P. gingivalis) activate Toll-like receptor (TLR) signaling, trigger NF-κB-mediated cytokine release (e.g., TNF-α, IL-1β, IL-6), and promote oxidative stress and Kupffer cell activation within the liver. The present systematic review summarized clinical evidence supporting these mechanistic links between periodontal pathogens and hepatic outcomes, highlighting the role of microbial crosstalk in liver pathophysiology. Methods: A PRISMA-compliant systematic review was conducted by searching PubMed, Scopus, and the Cochrane library, as well as gray literature. Eligible study designs were observational studies and trials evaluating P. gingivalis and other periodontal pathogens (Aggregatibacter actinomycetemcomitans, Prevotella intermedia, and Tannerella forsythia) for liver phenotypes (Non-Alcoholic Fatty Liver Disease [NAFLD]/Metabolic Dysfunction-Associated Steatotic Liver Disease [MASLD], fibrosis/cirrhosis, acute alcoholic hepatitis [AAH], and Hepatocellular carcinoma [HCC]). Risk of bias was assessed using the Newcastle-Ottawa Scale adapted for cross-sectional studies (NOS-CS) for observational designs and the RoB 2 scale for single randomized controlled trials (RCTs). Due to the heterogeneity of exposures/outcomes, results were summarized narratively. Results: In total, twenty studies (2012-2025; ~34,000 participants) met the inclusion criteria. Population-level evidence was conflicting (no clear association between anti-P. gingivalis serology and NAFLD), while clinical cohorts more frequently linked periodontal exposure, particularly to P. gingivalis, to more advanced liver phenotypes, including fibrosis. Microbiome studies suggested stage-related changes in oral communities rather than the effect of a single pathogen, and direct translocation into ascitic fluid was not observed in decompensated cirrhosis. Signals from interventional and behavioral research (periodontal therapy; toothbrushing frequency) indicate a potential modifiability of liver indices. The overall methodological quality was moderate with substantial heterogeneity, precluding meta-analysis. Conclusions: Current evidence supports a biologically plausible oral-liver axis in which periodontal inflammation, often involving P. gingivalis, is associated with liver damage. Causality has not yet been proven; however, periodontal evaluation and treatment may represent a low-risk option in periodontitis-associated NAFLD. Well-designed, multicenter prospective studies and randomized trials with standardized periodontal and liver measurements are needed.},
}

@article {pmid41294355,
year = {2025},
author = {O'Connor, JB and Fouquier, J and Neff, CP and Sterrett, JD and Marden, T and Fiorillo, S and Siebert, JC and Schneider, J and Nusbacher, N and Noe, AT and Fennimore, B and Higgins, J and Campbell, TB and Palmer, BE and Lozupone, C},
title = {Agrarian diet improves metabolic health in HIV-positive men with Prevotella-rich microbiomes: results from a randomized trial.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0118525},
doi = {10.1128/msystems.01185-25},
pmid = {41294355},
issn = {2379-5077},
abstract = {UNLABELLED: This study aimed to assess the impact of a high-fiber/low-fat agrarian diet (AD) on inflammation and metabolic outcomes in HIV-positive men who have sex with men (MSM). Since the gut microbiomes of MSM resemble those of individuals in agrarian cultures, including being Prevotella-rich and Bacteroides-poor, we hypothesized that they would have particularly strong health benefits from consumption of a diet matched to their microbiome type. Sixty-six participants, including 36 HIV-positive MSM [HIV(+)MSM], 21 HIV-negative MSM, and 9 HIV-negative men who have sex with women, were randomized to either an AD or a high-fat/low-fiber western diet (WD) for 4 weeks. Plasma, fecal, and colonic biopsy samples were obtained. Metabolic and inflammatory markers were measured in plasma. 16S ribosomal RNA sequencing was performed on fecal and biopsy samples, and shotgun metagenomic sequencing was performed on fecal samples. The AD reduced plasma low-density lipoprotein cholesterol (LDL-C) in HIV(+)MSM, with median reductions of 0.4138 mmoL/L at 2 weeks and 0.2845 mmol/L at 4 weeks. Greater LDL-C reductions were predicted by Prevotella-rich/Bacteroides-poor microbiomes with increased starch utilization potential, emphasizing the importance of personalized microbiome-dietary matching. The AD also reduced T cell exhaustion and pro-inflammatory intermediate monocytes and altered host transcription in the colonic mucosa.

IMPORTANCE: Our findings suggest tailoring diet interventions to baseline microbiome types can promote metabolic health in Prevotella-rich/Bacteroides-poor MSM, a significant portion of people living with HIV at risk for metabolic syndrome.This study was registered at NCT02610374.},
}

@article {pmid41294332,
year = {2025},
author = {Shubaita, M and Oneissi, M and Lindemann-Pérez, E and Fadhel Alvarez, C and Krachler, A-M and Proctor, DM and Pérez, JC},
title = {Diet-responsive genetic determinants of intestinal colonization in the yeast Candida albicans.},
journal = {mBio},
volume = {},
number = {},
pages = {e0243025},
doi = {10.1128/mbio.02430-25},
pmid = {41294332},
issn = {2150-7511},
abstract = {Dietary components influence microbial composition in the digestive tract. Although often viewed as energy sources, dietary components are likely to shape microbial determinants of intestinal colonization beyond metabolism. Here, we report that a dietary long-chain fatty acid enhances the yeast Candida albicans colonization of the murine gut partly by eliciting modifications to the fungal cell surface. Mice fed an oleic acid-rich diet were readily colonized by C. albicans and exhibited higher fungal load in feces compared with rodents fed an isocaloric control diet. Surprisingly, β-oxidation, a catabolic process to break down fatty acids for energy production, was dispensable for C. albicans to colonize the high oleic acid diet-fed mice. 16S rRNA analysis detected rather modest differences in the bacterial communities between control and oleic acid-rich diets. We identified SOK1 as an oleic acid-induced kinase that dictates cell wall mannan exposure and binding to intestinal mucin under anaerobic conditions. Furthermore, oleic acid induced the expression of several C. albicans transcription factors that positively regulate intestinal colonization via remodeling of the fungal cell surface. We posit that in environments largely devoid of oxygen like the large intestine, dietary oleic acid favors a C. albicans cell surface configuration that enhances gut occupation.IMPORTANCECandida albicans is a fungal pathobiont that inhabits the digestive tract of most human adults. The fungus has roles in health and disease because it modulates prominent immune-inflammatory host responses from the gut, and in individuals with debilitated defenses, it can disseminate from the gastrointestinal tract, producing life-threatening infections. Here, we investigate how a dietary component shapes C. albicans physiology and ultimately its ability to inhabit the mammalian gut.},
}

@article {pmid41294280,
year = {2025},
author = {Ullah, I and Zhou, D and Khan, AR and Muhammad, M and Zhang, Q and Ma, J and Egamberdieva, D and Shurigin, V and Li, L},
title = {Unveiling the Adaptation Mechanisms of Symbiotic Microbial Communities in Glycyrrhiza glabra Under Extreme Environmental Conditions.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf291},
pmid = {41294280},
issn = {1365-2672},
abstract = {Glycyrrhiza glabra is a medicinal legume species that is adapted to arid and saline environments, as well as climate stressors such as drought, salinity and extreme heat. This review highlights the latest developments in understanding the microbial communities associated with G. glabra, which enhance stress tolerance through nutrient acquisition, phytohormone modification, the production of antioxidants and osmotic regulation. This review synthesizes research on the distribution, diversity, and functionality of these microbial communities including endophytes, rhizobacteria, and arbuscular mycorrhizal fungi within the ecological context of degraded and marginal soils, which functionally enhances G. glabra as a model plant for studying plant-microbial interactions in extreme environments. We specifically highlight the microbial regulation of glycyrrhizin biosynthesis, a critical defense-related secondary metabolite with known therapeutic applications. Finally, we present an overview of new and emerging multi-omics tools that elucidate the molecular mechanisms underpinning these beneficial microbial interactions, and their potential in developing bio-inoculants for climate-resilient agriculture and providing a blueprint for harnessing native microbial partnerships to enhance plant survival, productivity, and soil restoration under climate uncertainty.},
}

@article {pmid41294086,
year = {2026},
author = {Vu, D and de Vries, M and van den Ende, BG and Houbraken, J and Nilsson, RH and Brankovics, B and Hernández-Restrepo, M and Groenewald, JZ and Crous, PW and Hagen, F and Meyer, W and Verkley, GJM and Groenewald, M},
title = {Advancing Yeast Identification Using High-Throughput DNA Barcode Data From a Curated Culture Collection.},
journal = {Molecular ecology resources},
volume = {26},
number = {1},
pages = {e70082},
doi = {10.1111/1755-0998.70082},
pmid = {41294086},
issn = {1755-0998},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Yeasts/classification/genetics/isolation & purification ; DNA, Fungal/genetics/chemistry ; High-Throughput Nucleotide Sequencing/methods ; DNA, Ribosomal Spacer/genetics/chemistry ; Sequence Analysis, DNA ; },
abstract = {Yeast identification is essential in fields ranging from microbiology and biotechnology to food science and medicine. While DNA barcoding has become the standard for identifying cultured strains, environmental DNA (eDNA) metabarcoding has revolutionised microbial community profiling, providing deeper insights into yeast communities across diverse ecosystems. A major challenge in DNA (meta)barcoding remains the limited availability of high-quality reference sequences, which are critical for accurate species identification and comprehensive taxonomic profiling of both environmental and clinical samples. To address this gap, the Westerdijk Fungal Biodiversity Institute (WI) launched a DNA barcoding initiative in 2006 to generate high-quality, often type-derived ITS and LSU barcodes for all ~100,000 fungal strains preserved in the CBS culture collection, including approximately 15,000 yeasts. Building on the yeast barcode dataset released in 2016, we now present an expanded set of 2856 ITS and 3815 LSU sequences, representing 911 and 1137 yeast species, respectively. Notably, 27%-29% of these sequences are derived from ex-type cultures. Using both newly generated and previously published barcodes, we assess the taxonomic resolution of commonly used yeast metabarcoding markers (ITS, ITS1, ITS2 and LSU) and propose marker-specific similarity cutoffs for different yeast taxonomic groups. These results provide actionable guidance for marker selection and improve the interpretation of metabarcoding data. We further demonstrate the impact of well-curated reference databases with up-to-date taxonomy by reanalyzing Human Microbiome Project data, revealing how diet and environment shape the gut mycobiota.},
}

*DNA Barcoding, Taxonomic/methods
*Yeasts/classification/genetics/isolation & purification
DNA, Fungal/genetics/chemistry
High-Throughput Nucleotide Sequencing/methods
DNA, Ribosomal Spacer/genetics/chemistry
Sequence Analysis, DNA

@article {pmid41293843,
year = {2025},
author = {Apostolidis, A and Da Silva, AS and Gray, T and Khullar, V and Mohamed-Ahmed, R and Papaefstathiou, E and Van den Ende, M and Wein, A and Abrams, P and Robinson, D},
title = {Is There Evidence of Diagnostic and Treatment Gaps for LUTS in Post-Menopausal Women With Genitourinary Syndrome of the Menopause? ICI-RS 2025.},
journal = {Neurourology and urodynamics},
volume = {},
number = {},
pages = {},
doi = {10.1002/nau.70173},
pmid = {41293843},
issn = {1520-6777},
support = {//The authors received no specific funding for this work./ ; },
abstract = {AIMS: This report, from the International Consultation on Incontinence-Research Society, aims to evaluate the existing evidence and identify diagnostic and treatment gaps for Lower Urinary Tract Symptoms (LUTS) in post-menopausal women with Genitourinary Syndrome of Menopause (GSM).

METHODS: An overview on the current literature, including pathophysiology, diagnosis and management of GSM associated LUTS, including incontinence, overactive bladder, underactive bladder and recurrent urinary tract infections (rUTIs).

RESULTS: Significant gaps in the literature were identified. GSM is underdiagnosed and the interplay between hormonal changes in the postmenopausal period on LUTS remains poorly understood. Diagnostic methods for rUTIs lack sensitivity and the role of the urinary microbiome is emerging. Current treatments, including topical oestrogens and systemic hormone therapy, lack long-term efficacy data on LUTS. Evidence for regenerative medicine techniques remain limited by low-quality studies and short-term follow up.

CONCLUSION: There is lack of high-quality evidence, which hinders the optimal management of LUTS in post-menopausal women with GSM. The panel proposes targeted research questions, focusing on the hormonal impact on the lower urinary tract, advancing diagnostics and robust clinical trials for existing and novel therapies, to bridge current gaps in the literature and improve patient care.},
}

@article {pmid41293836,
year = {2025},
author = {Devesa-Aranguren, I and González-Sanz, C and Gutiérrez-Manso, L and Lozano-Enguita, A and Morillas-Montávez, A and Torregrosa Gómez-Meana, I and Del Pozo, JC and Caro, E and Cabrera, J},
title = {Root and microbiome synergy in plant heat stress resilience: epigenetic regulation as a frontier for future research.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/eraf520},
pmid = {41293836},
issn = {1460-2431},
abstract = {Rising temperatures driven by climate change put crops under stress and threaten their productivity by exacerbating both abiotic and biotic challenges. While research has traditionally focused on aboveground plant responses, this review focuses on the often-overlooked role of roots in heat stress adaptation. Its primary objective is to synthesize current knowledge on how root development and root-microbiome interactions contribute to plant resilience under elevated atmospheric temperatures. The interest in this topic is driven by growing evidence that belowground traits play a pivotal role in determining plant performance under thermal stress. In addition, new findings indicate that epigenetic regulation might influence root development and microbial effects to significantly enhance heat tolerance. Additionally, we emphasize how experimental research often underscores the importance of using experimental approaches, whether in vitro or in greenhouses, that better replicate natural conditions to ensure the translational relevance of laboratory findings. By integrating physiological, molecular, and ecological insights, this review offers insights for the development of more heat-resilient crops in the face of a warming climate scenario.},
}

@article {pmid41293657,
year = {2025},
author = {Khazi, AI and Ahmad, A},
title = {Gut-Immune Interplay: Decoding the Microbiome's Impact on Immunity and Diseases.},
journal = {Journal of pharmacy & bioallied sciences},
volume = {17},
number = {3},
pages = {108-116},
pmid = {41293657},
issn = {0976-4879},
abstract = {The gut microbiome is a critical regulator of local and systemic immunity with downstream consequences on immune functions and health of the host. Coevolution with the host bolsters the development and performance of the immune system, particularly during early life, and also plays roles in immune responses in adulthood. Alterations in the gut microbiome, whether as a result of antibiotics, diet, or environmental manipulation, can also drive inappropriate immune responses and predisposition to infections and inflammatory and autoimmune diseases. Since the microbiome impacts systemic immunity, microbial products stemming from the gut can alter immunity in far-flung tissues. Recent studies have emphasized the therapeutic promise of probiotics due to their ability to modulate gut microbiota and improve immune system activity and symptoms as well as prognosis of different diseases. Aging is one of the key risk factors for several age-related conditions, where the immune system and gut microbiome are major culprits, further explaining the importance of microbiome health across the life course. This emerging approach of microbiome modulation is opening up new pathways for combating infectious diseases, including both antibiotic-resistant infections and viral disease. This review highlights the interdependent nature of the gut microbiome and immune health, with significant ramifications for disease prevention and treatment.},
}

@article {pmid41293546,
year = {2025},
author = {English, CJ and Manoj, M and Henderson, LC and Opalk, K and Carlson, CA},
title = {Seasonal and developmental stage changes in mucilage carbohydrate content shape the kelp microbiome.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf197},
pmid = {41293546},
issn = {2730-6151},
abstract = {A large amount of a photoautotroph's fixed carbon is released as dissolved organic matter, from both exudation and solubilized detritus. This dissolved material contributes to a surface mucilage layer that shapes their immediate environment, including the composition of their microbiome. Here we evaluated the microbiome and mucilage carbohydrate composition of Macrocystis pyrifera (giant kelp), a globally distributed foundation species, in response to seasonal nutrient availability and developmental stage. We combine 16S rRNA amplicon analysis of the giant kelp microbiome with carbohydrate monomer analysis of kelp mucilage to examine microbe-mucilage relationships. We found significant differences in the microbiome and mucilage composition between seasons and developmental stages of giant kelp. Higher tissue-nitrogen content in the spring coincided with elevated amounts of glucosamine, a nitrogen-containing sugar, in giant kelp mucilage, while senescence led to the release of mannuronic acid, an alginate indicator. The release of glucosamine and fucose-rich mucilage was correlated with an increase in the relative abundance of bacteria within the Planctomycetota phylum, whereas mannuronic acid-rich mucilage coincided with an increase in the relative abundance of members of the Flavobacteriia and Gammaproteobacteria lineages. We investigated putative carbohydrate-microbe relationships by isolating a member of the Planctomycetota phylum from the surface of giant kelp. Using whole genome analysis and growth assays, we demonstrate that this isolate grows on fucoidan and N-acetyl glucosamine, but not alginate, consistent with the observed relative abundance of this clade in the kelp microbiome in response to variable mucilage carbohydrate content. This suggests a key role of kelp mucilage carbohydrate composition in structuring its microbiome as has been observed for other organisms such as corals and within the human gut.},
}

@article {pmid41293310,
year = {2025},
author = {Martignoni, MM and Garnier, J and Tyson, RC and Harris, KD and Kolodny, O},
title = {Towards a theory of microbially-mediated invasion encompassing parasitism and mutualism.},
journal = {Biological invasions},
volume = {27},
number = {12},
pages = {253},
pmid = {41293310},
issn = {1387-3547},
abstract = {UNLABELLED: Biological invasions pose major ecological and economic threats, and extensive research has been dedicated to understanding and predicting their dynamics. Most studies focus on the biological invasion of single species, and only in recent years has it been realized that multi-species interactions that involve native and invasive host species and their microbial symbionts can play important roles in determining invasion outputs. A theoretical framework that treats these interactions and their impact is lacking. Here we offer such a framework and use it to explore possible dynamics that may emerge from the sharing of native and non-native symbionts among native and non-native host species. Thus, for example, invasive plants might benefit from native microbial communities in the soil, or might be particularly successful if they carry with them parasites to which competing native hosts are susceptible. On the other hand, invasion might be hindered by native parasites that spread from native to invasive individuals. The mathematical framework that we present in this study provides a new mechanistic, cohesive, and intuition-enhancing tool for theoretically exploring the ways by which the subtleties of host-microbe relationships can influence invasion dynamics. We identify multiple pathways through which microbes can facilitate (or prevent) host invasion, microbial invasion, and the invasion of both hosts and their co-introduced microbes. We disentangle invasion outcomes and suggest possible ecological dynamics that may be underexplored in current invasion biology literature. Our work sets the foundations for invasion theory that includes a community-level view of invasive and native hosts as well as their microbial symbionts.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10530-025-03711-4.},
}

@article {pmid41293165,
year = {2025},
author = {Wen, J and Liang, H and Zhao, M and Xuan, B and Meng, X and Liu, Y and Wang, L and He, L and Zhou, T and Tao, Y and Wang, Y},
title = {Harnessing the gut microbiome to modulate ferroptosis: a metabolic strategy for the treatment of digestive tract cancers.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1703964},
pmid = {41293165},
issn = {1664-3224},
mesh = {*Ferroptosis ; Humans ; *Gastrointestinal Microbiome ; *Gastrointestinal Neoplasms/metabolism/therapy/microbiology/pathology ; Animals ; },
abstract = {Ferroptosis is a form of regulated cell death defined in recent years, characterized by iron-dependent accumulation of lipid peroxides. A large body of research has demonstrated that ferroptosis is closely associated with the progression of gastrointestinal tumors (such as gastric cancer, colorectal cancer, and esophageal cancer), and gastrointestinal tumor cells exhibit unique sensitivity to ferroptosis. This indicates that ferroptosis has emerged as a highly promising strategy to combat therapy-resistant colorectal cancer. Although the intrinsic ferroptosis-suppressive and ferroptosis-promoting pathways in gastrointestinal tumors have been fully elucidated, the current understanding of the extrinsic metabolites and pathways that regulate ferroptosis in the pathogenesis of gastrointestinal tumors remains relatively limited. Emerging studies have shown a strong link between gut microbial metabolism and the progression of gastrointestinal tumors. This review summarizes the relevant aspects of gut microbiota metabolism, explores how these gut microbiota-derived metabolites regulate cancer progression through ferroptosis, and proposes that targeting gut microbiota-mediated ferroptosis represents a potential therapeutic approach for gastrointestinal tumors.},
}

*Ferroptosis
Humans
*Gastrointestinal Microbiome
*Gastrointestinal Neoplasms/metabolism/therapy/microbiology/pathology
Animals

@article {pmid41293163,
year = {2025},
author = {Li, G and Xiong, Y and Li, Z and Yu, Q and Li, S and Xie, J and Zeng, S and Yu, D and Yang, Y and Yu, J},
title = {Gut microbiota-derived metabolites modulate Treg/Th17 balance: novel therapeutic targets in autoimmune diseases.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1710733},
pmid = {41293163},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Autoimmune Diseases/immunology/therapy/metabolism/microbiology ; *T-Lymphocytes, Regulatory/immunology/metabolism ; *Th17 Cells/immunology/metabolism ; Animals ; Fatty Acids, Volatile/metabolism ; },
abstract = {Dysregulation of the homeostasis between regulatory T cell (Treg) and T helper 17 cell (Th17) is increasingly recognized as a pivotal mechanism in the pathogenesis of autoimmune diseases. Emerging evidence indicates that gut microbiota-derived metabolites, including short-chain fatty acids, secondary bile acids, and aromatic metabolites, modulate Treg/Th17 balance by shaping immune cell differentiation and function, thereby revealing novel therapeutic opportunities. This Review synthesizes recent clinical and preclinical findings on the influence of microbial communities and their metabolites on Treg/Th17 dynamics and examines the underlying mechanisms in representative autoimmune disorders, such as rheumatoid arthritis, systemic lupus erythematosus, Graves' disease, autoimmune hepatitis, and myasthenia gravis. We critically evaluate current microbiome-targeted interventions and discuss their translational potential, highlighting both promises and challenges. Finally, we outline priorities for future research, focusing on multi-omic integration, the development of individualized therapeutic strategies, and rigorous clinical evaluation, to facilitate the development of safe and effective microbiota-based therapies for autoimmune diseases.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Autoimmune Diseases/immunology/therapy/metabolism/microbiology
*T-Lymphocytes, Regulatory/immunology/metabolism
*Th17 Cells/immunology/metabolism
Animals
Fatty Acids, Volatile/metabolism

@article {pmid41293001,
year = {2025},
author = {Mehl, LC and Nuñez, MS and Sanz, JM and Geraghty, A and Dal Cengio, L and Kaval, A and Chen, Y and Gibson, EM},
title = {Environmental factors contribute to cancer therapy toxicity.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.11.687867},
pmid = {41293001},
issn = {2692-8205},
abstract = {Cancer therapy-related cognitive impairment (CRCI) affects numerous cancer patients, however there is substantial variability in its severity. Here, we investigated how environmental factors such as housing facility and time of treatment, known as chronotherapy, impact chemotoxicity in a pediatric murine model of methotrexate (MTX)-induced CRCI. We find that MTX consistently impacts body mass in a time-of-day specific manner across different housing facilities. Intriguingly, investigation of the gut microbiome acutely after MTX chronotherapy revealed substantial differences in microbial composition between animals housed in different facilities as well as decreased microbial diversity at different times of day. Furthermore, these differences in the gut microbiome after MTX chronotherapy coincide with differences in circulating inflammatory cytokine profiles between facilities and times of day. Chronically, housing facility continued to impact serum cytokine levels after MTX treatment, whereas the effect of time wanes. Nonetheless, we found that time drastically alters chronic white matter microglial gene expression in the central nervous system (CNS) after MTX treatment. Together, these findings demonstrate that both housing facility and time dictate response to MTX chronotherapy in the periphery and CNS. Collectively, this work elucidates putative factors that can regulate MTX-induced chemotoxicity.},
}

@article {pmid41292989,
year = {2025},
author = {Moreno-Gamez, S and Anderson, BW and Vercelli, GT and Altmann, F and Goodman, AL and Cordero, OX},
title = {Niche partitioning by resource size in the gut microbiome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.13.688124},
pmid = {41292989},
issn = {2692-8205},
abstract = {Niche partitioning promotes diversity of the human gut microbiota. However, the molecular basis of resource specialization and niche separation in the gut remains poorly understood. Here we show that structural differences in glycan transporters drive members of the genus Bacteroides, common human gut commensals, to specialize on distinct chain lengths of the same fructan molecule. While species encoding canonical SusCD systems for glycan import formed by a membrane-embedded barrel capped with a lipoprotein lid specialized in long-chain fructans, species with smaller lidless transporters, not previously described in Bacteroides, specialized in short-chain fructans. Strikingly, we found that a ~140-amino acid domain in the SusC barrel is a structural feature that governs substrate preference: deleting it does not impair transport but instead shifts uptake preferences from long- to short-chain fructans. These structural differences predict competitive outcomes in vivo on fructans of varying lengths, suggesting that glycan uptake mechanisms shape ecological niches in the gut and can inform fiber-based dietary interventions. Similar small lidless transporters exist across the Bacteroidota, expanding the paradigm of glycan utilization in this phylum beyond the canonical SusCD architecture.},
}

@article {pmid41292897,
year = {2025},
author = {Maan, H and Jogia, W and Duan, C and Matheis, F and Nishimoto, EK and Zhang, C and Sullivan, AP and Schluter, J},
title = {Sugar ABC transporter repertoires predict ecological dynamics in gut microbiome communities.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.12.686590},
pmid = {41292897},
issn = {2692-8205},
abstract = {The gut microbiome plays a central role in human health, but modern diets and lifestyles alter its composition. The microbial genomic traits that drive these ecological shifts, particularly in response to dietary sugars, remain poorly characterized. Here, we integrate a large dataset of longitudinal human diet-microbiome records and comparative genomics of human and murine gut isolates with in vitro and in vivo experiments to identify sugar ABC (ATP-binding cassette) transporters as key predictors of bacterial fitness and microbial community responses to dietary sugars. Strains encoding these transporters exhibit enhanced growth and consistently outcompete others in both monocultures and complex consortia across contexts. In gnotobiotic mice, dietary sugar supplementation selectively increases the expansion of sugar ABC transporter-positive bacteria, including the model gut pathobiont Escherichia coli . Systematic deletion of sugar transporter genes in E. coli revealed that a specific sugar ABC transporter gene was required to invade a model gut consortium, highlighting its importance in microbial competition. Together, these findings establish sugar ABC transporters as genomic predictors of microbial community dynamics in response to dietary sugars.},
}

@article {pmid41292823,
year = {2025},
author = {Rodriguez, JS and Hera, MR and Koslicki, D},
title = {Leveraging FracMinHash Containment for Genomic d N / d S.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.12.688019},
pmid = {41292823},
issn = {2692-8205},
abstract = {UNLABELLED: Increasing availability of genomic data demands algorithmic approaches that can efficiently and accurately conduct downstream genomic analyses. These analyses, such as evaluating selection pressures within and across genomes, can reveal developmental and environmental pressures. One such commonly used metric to measure evolutionary pressures is based on the ratio of non-synonymous and synonomous substitution rates, d N / d S . Conventionally, the d N / d S ratio is used to infer selection pressures employing alignments to estimate total non-synonymous and synonymous substitution rates along protein-coding genes. However, this process can be time consuming and not scalable for larger datasets. Recently, a fast, approximate similarity measure, FracMinHash containment, was introduced and related to average nucleotide identity. In this work, we show how FracMinHash containment can be used to quickly estimate d N / d S enabling alignment-free estimations at a genomic level. Through simulated and real world experiments, our results indicate that employing FracMinHash containment to estimate d N / d S is scalable, enabling pairwise d N / d S estimations for 85,205 genomes within 5 hours. Furthermore, our approach is comparable to traditional d N / d S methods, representing sequences subject to positive and negative selection across various mutation rates. Moreover, we used this model to evaluate signatures of selection between Archaeal and Bacterial genomes, identifying a previously unreported metabolic island between Methanobrevibacter sp . RGIG2411 and Candidatus Saccharibacteria bacterium RGIG2249. We present, FracMinHash d N / d S , a novel alignment-free approach for estimating d N / d S at a genome level that is accurate and scalable beyond gene-level estimations while demonstrating comparability to conventional alignment-based d N / d S methods. Leveraging the alignment-free similarity estimation, FracMinHash containment, pairwise d N / d S estimations are facilitated within milliseconds, making it suitable for large-scale evolutionary analyses across diverse taxa. It supports comparative genomics, evolutionary inference, and functional interpretation across both synthetic, and complex biological datasets.

A version of the implementation is available at https://github.com/KoslickiLab/dnds-using-fmh.git . The reproduction of figures, data, and analysis can be found at https://github.com/KoslickiLab/dnds-using-fmh_reproducibles.git .

CONTACT: dmk333@psu.edu.

SUPPLEMENTARY INFORMATION: Supplementary data are available at PLOS Computational Biology online.

AUTHOR SUMMARY: Understanding how evolution shapes genomes helps us learn about the pressures organisms face in their environments. Scientists traditionally measure this by comparing genetic changes that alter proteins versus those that don't, a ratio that reveals whether natural selection is preserving or changing genes. However, this conventional approach requires computationally intensive sequence alignments, making it impractical for analyzing the massive genomic datasets now available. We developed a faster, alignment-free method to estimate evolutionary pressure across entire genomes. Our approach uses a computational technique called FracMinHash that compresses genomic information while preserving meaningful patterns. We tested our method on both simulated and real-world data, including over 85,000 microbial genomes, completing the analysis in just five hours whereas traditional methods would take days or weeks for the same analysis. The results were comparable to traditional methods and correctly identified genes under different types of selection. Using this approach, we discovered a previously unreported shared genetic region between an archaeal and bacterial species from the goat gut microbiome, suggesting ancient gene transfer between these distant branches of life. Our method makes large-scale evolutionary analysis practical for diverse applications, from tracking microbial strains to understanding adaptation in complex microbial communities, potentially accelerating discoveries in comparative genomics and evolutionary biology.},
}

@article {pmid41292709,
year = {2025},
author = {Quiñones-Sanchez, CL and Bilbao-Del Valle, JL and Urdaneta-Colon, MA and Santiago-Rodriguez, TM and Rodriguez-Fernandez, IA},
title = {Optimizing Tissue Lysis and DNA Extraction Protocols to Enhance Bacterial Diversity Profiling in the Drosophila melanogaster Gut Microbiome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.15.688634},
pmid = {41292709},
issn = {2692-8205},
abstract = {The gut microbiota is a dynamic community that influences host metabolism, immunity, and overall health. Accurate characterization of this community requires robust and reproducible DNA extraction methods; however, technical biases introduced during tissue lysis and DNA isolation remain major challenges in microbiome research, particularly in animal model systems. In this study, we compared two commercial DNA extraction kits (Qiagen and Zymo) and two lysis methods (manual pestle homogenization and bead-beating) to evaluate their impact on microbiota profiling in a microbial community standard (MCS) and Drosophila melanogaster gut samples, a tractable model for host-microbe interactions. Full-length 16S rRNA sequencing was performed using Oxford Nanopore Technologies, followed by bioinformatic analysis using EPI2ME for taxonomic classification and standard diversity pipelines. Our data revealed that extraction and lysis methods significantly influence microbial composition, with some protocols resulting in inflated richness in MCS samples. Pestle homogenization with the Qiagen kit yielded the highest bacterial species richness while maintaining consistent representation of both Gram-positive and Gram-negative taxa. These findings demonstrate that extraction methodology strongly affects microbial diversity estimates and emphasize the need for standardized protocols to ensure reproducibility across microbiome studies, particularly those using model systems.},
}

@article {pmid41292685,
year = {2025},
author = {O'Brien, JM and Blais, ND and Holland-Moritz, H and Shek, KL and Douglas, TA and Barbato, RA and Ernakovich, JG},
title = {Consistent microbial responses during the aerobic thaw of Alaskan permafrost soils.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1654065},
pmid = {41292685},
issn = {1664-302X},
abstract = {Arctic systems are warming at four times the global average, causing permafrost-permanently frozen soil, ice, organic matter, and bedrock-to thaw. Permafrost thaw exposes previously unavailable soil carbon and nutrients to decomposition-a process mediated by microbes-which releases greenhouse gases such as carbon dioxide and methane into the atmosphere. While it is well established that thaw alters the composition and function of the permafrost microbiome, patterns revealing common responses to thaw across different permafrost soil types have not yet emerged. In this study, we address how permafrost thaw impacts microbiome diversity, alters species abundance, and contributes to carbon flux in the Arctic. We sampled peat-like, mineral, and organic-mineral permafrost from three locations in central and northern Alaska. We assessed their abiotic soil properties and microbiome characteristics before and after a 3-month laboratory microcosm incubation. Across all sites, prokaryotic biomass increased following thaw, measured as 16S rRNA gene copy number. This change in biomass was positively correlated with cumulative respiration, indicating an increase in microbial activity post-thaw. We evaluated the thaw response of microbial taxa across three sites, identifying taxa that significantly increased in abundance post-thaw. Common responders shared across all sites belonged to the families Beijerinckiaceae, Burkholderiaceae, Clostridiaceae, Oxalobacteraceae, Pseudomonadaceae, and Sporichthyaceae, indicating a common set of taxa that consistently respond to thaw regardless of site-specific conditions. Alpha diversity decreased with thaw across all sites, likely reflecting the increased dominance of specific thaw-responsive taxa that may be driving post-thaw biogeochemistry and increased respiration. Taken together, we deepen the understanding of different permafrost microbiomes and their response to thaw, which has implications for the permafrost-climate feedback and enables more accurate predictions of how Arctic ecosystem structure and function respond to change.},
}

@article {pmid41292684,
year = {2025},
author = {Liu, J and Sha, Y and Dang, R and Zhou, L and Zhou, M and Tan, Y and Wang, J and Ran, G and Xie, W and Xia, D and Wang, L and Zhao, X and Goi, BM and Yu, J and Xiao, L},
title = {Acetate-based syntrophy enhances methane production potential of ruminant feces.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1706620},
pmid = {41292684},
issn = {1664-302X},
abstract = {Livestock feces contribute to approximately 32% of global methane emissions. Although ruminants are generally believed to have a higher methane production potential than non-ruminants, the dominant pathways and key regulatory processes underlying methane generation in ruminants remain poorly understood, impeding effective manure management and accurate livestock emission assessments. In this study, metagenomic and carbon isotope techniques were employed to investigate methane production potential and key pathways in sheep, pig, chicken, and duck feces. Methane production potential of ruminant sheep feces was significantly higher (approximately threefold) compared to that of non-ruminants. Isotopic analysis of methane sources revealed that sheep feces primarily produce methane through the acetoclastic pathway, whereas the other three likely rely on CO2 reduction. Metagenomic analysis of methanogenic pathways further indicated that the abundance of functional genes associated with acetoclastic methanogenesis is significantly higher in sheep feces compared to the other three. Moreover, the co-occurrence network analysis highlighted a tightly coordinated, cross-species partnership between fermentative acetogenic bacteria and methanogenic archaea in the sheep fecal microbiome. Together, our findings provide insights into some key methanogenic pathways, such as acetoclastic methanogenesis, contributing to high methane production from ruminant feces.},
}

@article {pmid41292682,
year = {2025},
author = {Nagaraju, Y and Triveni, S and Srinvas Rao, T and Cardinale, M},
title = {Editorial: Exploring pollen microbiome: implications for plant physiology, crop improvement and human allergies.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1717890},
pmid = {41292682},
issn = {1664-302X},
}

@article {pmid41292680,
year = {2025},
author = {Park, MA and Son, S and Lim, DJ and Yu, HS and Yoon, YH and Kim, SH and Lee, SS and Kim, DH and Kim, Y},
title = {Effects of the monolaurin based feed additive MGOsyn on methane production, rumen fermentation, and microbial communities using rumen fluid from Hanwoo steers in an in vitro study.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1699688},
pmid = {41292680},
issn = {1664-302X},
abstract = {Reducing enteric methane emissions from livestock mitigates environmental impact and improves production efficiency. This initial in vitro study investigated the potential of MGOsyn, a new feed additive composed of monolaurin, garlic, and oregano with synergistic antimethanogenic properties, to influence rumen fermentation parameters, methane production, and the structure of bacterial and archaeal communities. The experiment was conducted as a batch culture using rumen fluid collected from Hanwoo steers with ground concentrate as the substrate. MGOsyn, a monolaurin based feed additive (GRAS, Generally Recognized As Safe), was supplemented at three different concentrations. 0% (MGOsyn CON), 0.1% (MGOsyn LOW), and 0.2% (MGOsyn HIGH) of the total fermentation volume. After 24 h of incubation at 39 °C, MGOsyn increased propionate production by 50% in a dose dependent manner, while reducing methane emission by 61%, acetate proportion and the acetate to propionate ratio. Microbial community analyses revealed that MGOsyn effectively altered the ruminal microbiome. The bacterial community exhibited an increased relative abundance of succinate and propionate producing bacteria, such as Succinivibrio, Succiniclasticum, Candidatus Saccharimonas, Succinivibrionaceae UCG-002, and Prevotella 7 which are involved in hydrogen sink pathways following MGOsyn supplementation. Considering the archaeal community, the abundance of Methanomethylophilaceae decreased with MGOsyn supplementation compared with that in the control, whereas Methanosphaera increased in the high MGOsyn supplementation group. To further explore the underlying mechanisms of methane mitigation, we performed correlation and intercorrelation analyses between fermentation parameters and microbial taxa, along with functional predictions of relevant metabolic pathways. Succinate/propionate producing bacteria showed strong positive correlations with MGOsyn supplementation and propionic acid production, and strong negative correlations with acetic acid production, the acetate to propionate ratio, and methane production. These findings suggest that MGOsyn effectively mitigates methane emissions by stimulating propionate formation through the hydrogen sink pathway. By altering the ruminal microbial community toward enhanced propionate production, MGOsyn shows promise as a functional feed additive for improving rumen fermentation efficiency and reducing methane output in ruminants.},
}

@article {pmid41292576,
year = {2025},
author = {Ayeke, DY and Osei-Poku, P and Byamukama, D and Amewu, EKA and Abakah, A and Shardow, ALK and Yeboah, SMA and Antwiwaa, C and Wilson, MB and Wireko, S and Larbi, A and Kwarteng, A},
title = {Molecular Characterisation of Fungi Populations in the Chronic Wounds of Filarial Lymphedema Patients in Southern Ghana: A Cross-Sectional Study.},
journal = {Health science reports},
volume = {8},
number = {11},
pages = {e71552},
pmid = {41292576},
issn = {2398-8835},
abstract = {BACKGROUND AND AIMS: Lymphatic filariasis (LF) and associated chronic wounds are of public health concern worldwide. Despite the significant burden of lymphatic filariasis (LF) and its associated chronic wounds, the fungal component of the wound microbiome remains poorly understood. Previous research has primarily focused on bacterial pathogens, neglecting the potential role of fungi in wound pathogenesis and progression. A comprehensive understanding of the microbial landscape, especially the overlooked fungal component, is crucial for developing effective prevention and treatment strategies. The study aimed to molecularly characterize the fungal populations present in these wounds via Internal Transcribed Spacer (ITS) sequencing.

METHODS: This was a cross-sectional study, with a total of 63 individuals sampled from eight (8) LF-hyperendemic communities within the Ahanta West District in Ghana. Skin and wound swabs were collected from each participant between December 2021 and February 2022 and subjected to standard culture-based techniques. Fungal isolates were identified, and their DNA was extracted for subsequent PCR amplification of the ITS region. The sequencing was performed using the Oxford Nanopore platform.

RESULTS: Of the 63 patients sampled, fungal colonies were observed in 16 individuals (25.4% prevalence) through culture-based methods. Molecular characterisation identified 24 Twenty-four (24) distinct fungal species at different frequencies from nine different genera: Cladosporium, Aspergillus, Periconia, Penicillium, Candida, Lasiodiplodia, Acrophialophora, Zygosporium, and Trichoderma. Cladosporium spp. was the most prevalent, accounting for 30% of isolates, followed by Aspergillus spp. (28.6%), Periconia spp. (14.3%), Penicillium spp. (12.9%), and Candida spp. (8.6%). A smaller proportion of isolates represented Lasiodiplodia spp., Acrophialophora spp., Zygosporium spp., and Trichoderma spp., each comprising 1.4% of the total isolates. Notably, only 2 out of the 16 patients did not present with mixed fungal populations in their wounds.

CONCLUSIONS: The presence of fungal pathogens and the potential for polymicrobial infections within the LF-wound environment highlight the need for comprehensive and tailored treatment protocols. Effective wound management is essential to address these complex wounds and mitigate the development of antibiotic resistance, a growing concern in chronic wound care.},
}

@article {pmid41292506,
year = {2025},
author = {Arawker, MH and Habibullah, F and Baral, S and Fu, L and Sun, N and Li, H and Ji, F and Qiu, X},
title = {Microbiome Mediated Immune Crosstalk on the Gut-Thyroid Axis in Autoimmune Thyroid Disease.},
journal = {Immunological investigations},
volume = {},
number = {},
pages = {1-21},
doi = {10.1080/08820139.2025.2593335},
pmid = {41292506},
issn = {1532-4311},
abstract = {BACKGROUND: The gut microbiota plays an important role in systemic immune homeostasis and is increasingly implicated in autoimmune thyroid disease (AITD). Evidence suggests that gut dysbiosis, impaired intestinal barrier function, and altered microbial metabolites particularly short-chain fatty acids contribute to immune imbalance along the gut-thyroid axis. Although molecular mimicry between microbial and thyroid antigens has been proposed, current human evidence remains associative rather than causal.

METHODS: This review synthesized current observational, translational, and preclinical studies evaluating microbial composition, barrier integrity, microbial metabolites, and immune pathways relevant to AITD. Mechanistic insights into T-lymphocyte regulation and microbial-host interactions were integrated with emerging interventional data.

RESULTS: Gut dysbiosis in AITD is linked to reduced regulatory T-lymphocytes, expansion of Th17 cells, increased intestinal permeability, and the loss of short-chain-fatty-acid-producing taxa. Observational studies consistently report disease-associated taxonomic alterations, while preclinical models support causal pathways through barrier disruption and microbiota-driven immune activation. Early interventional approaches such as high-fiber dietary patterns, probiotics, prebiotics, and experimental fecal microbiota transplantation show modest reductions in thyroid autoantibodies in small trials, though effects are strain-specific, short-term, and not disease-modifying.

CONCLUSION: Despite largely associative human evidence, converging mechanistic findings highlight the gut microbiota as a modifiable contributor to thyroid autoimmunity. Future priorities include clarifying causality, identifying keystone microbial taxa and metabolites, and establishing standardized interventional frameworks to facilitate translation into endocrine practice.},
}

@article {pmid41292129,
year = {2025},
author = {Azar, S and Rehermann, B},
title = {The role of immune responses and microbiota in adipose tissue homeostasis.},
journal = {The Journal of physiology},
volume = {},
number = {},
pages = {},
doi = {10.1113/JP286422},
pmid = {41292129},
issn = {1469-7793},
support = {DK054508/DK/NIDDK NIH HHS/United States ; },
abstract = {White and brown adipose tissue form a metabolic organ that plays a crucial role in regulating body energy homeostasis. Adipose tissue is richly vascularized and innervated to respond to a variety of environmental signals. Adipose tissue also contains diverse populations of innate and adaptive immune cells. These immune cells contribute to the regulation of adipose tissue function, and adipocytes in turn signal to immune cells in response to metabolic and environmental triggers. The gut microbiota have recently emerged as an additional factor that affects adipose tissue homeostasis. This can occur either directly via metabolites and bacterial products or indirectly via its effects on immune cells. Natural, co-evolved microbiota, if encountered in early postnatal life, have been shown to confer protection against obesity in later periods of life. The complexity of these factors and interactions warrants further investigation and may ultimately provide opportunities for therapeutic interventions that prevent obesity and metabolic disease.},
}

@article {pmid41292096,
year = {2025},
author = {Graves, DT and Levine, MA and Aldosary, S and Demmer, RT},
title = {Understanding the Periodontitis-Diabetes Linkage: Mechanisms and Evidence.},
journal = {Journal of dental research},
volume = {},
number = {},
pages = {220345251388340},
doi = {10.1177/00220345251388340},
pmid = {41292096},
issn = {1544-0591},
abstract = {Diabetes mellitus (DM) and periodontitis share a complex, bidirectional relationship, with each condition exacerbating the other. Diabetes, particularly when poorly controlled, significantly increases the risk, severity, and progression of periodontitis. The biological mechanisms involved are complex and numerous. Hyperglycemia in diabetes is linked to oral microbial dysbiosis, which is in turn associated with increased inflammation, epithelial barrier dysfunction, impaired neutrophil and macrophage function, altered T-cell profiles, and cytokine imbalance, collectively fostering chronic inflammation and immune dysregulation. Moreover, diabetes alters bone metabolism, promoting osteoclastogenesis and reducing reparative bone regeneration by limiting coupled bone formation through an effect on growth factor production, mesenchymal stems cells, and osteoblasts. Conversely, periodontitis is strongly linked to poor glycemic control. Clinical studies and longitudinal meta-analyses report consistent positive associations, while randomized controlled trials show that periodontal therapy reduces HbA1c by ~0.43%. Emerging evidence suggests that periodontitis and oral preclinical dysbiosis contribute to diabetogenesis, although causality remains uncertain. Periodontitis may drive metabolic dysfunction through several biological mechanisms. The dysbiotic oral microbiome and subsequent periodontitis may promote systemic inflammation and subsequent insulin resistance and glucose intolerance. Moreover, oral dysbiosis may deplete nitrate-reducing taxa and impair nitric oxide pathways, which has relevance to both periodontal and cardiometabolic health. Accordingly, periodontal treatment in diabetic populations has shown potential health care savings. Nevertheless, trials assessing the influence of periodontitis treatment on systemic outcomes consistently show significant treatment heterogeneity, which requires explication in future studies. This review underscores the systemic implications of periodontitis in diabetes and highlights the value of integrating periodontal care into diabetes management. A better understanding of the shared pathophysiology between these diseases supports interdisciplinary approaches and points toward novel preventive and therapeutic strategies targeting inflammation, microbial balance, and host response modulation to jointly benefit periodontal and cardiometabolic health.},
}

@article {pmid41292093,
year = {2025},
author = {Ji, Y and Zhang, Y and Ma, Y and Xu, L and Chen, X and Fang, W and Li, Y and Yan, D and Cao, A and Wang, Q},
title = {Fumigant-mediated suppression of Xanthomonas in mango replant soils: linking mango bacterial angular spot disease to rhizosphere and phyllosphere microbiome restructuring.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.70402},
pmid = {41292093},
issn = {1526-4998},
support = {2023YFD1701200//National Key Research and Development Program of China/ ; YDLH03//Hainan Local Economic Development Project - Construction of a Mango Pest and Disease Prevention and Control System/ ; },
abstract = {BACKGROUND: Mango bacterial angular spot disease, caused by a bacterial pathogen, increasingly threatens mango production and has become a significant bottleneck to the sustainable development of the mango industry. The pathogen can spread through air and soil, but the impact of these transmission routes on the microbial community structures in the rhizosphere and phyllosphere remains unclear. Understanding how this disease alters microbial dynamics is crucial for developing effective management strategies.

RESULTS: The disease significantly disrupted both rhizosphere and phyllosphere microbial communities, with a decrease in diversity and a reduction in beneficial microbes. Fumigation effectively reduced the abundance of the mango bacterial angular spot pathogen, with ethylicin showing the strongest effect. In addition, fumigation enhanced the competitive advantage of beneficial microbes, with the relative abundance of Bacillus and Lecanicillium rising by more than 60%. Fumigation reshaped the microbial communities, with fungal communities in both the rhizosphere and phyllosphere returning to a healthier state and bacterial communities undergoing dynamic adjustments. In particular, Proteobacteria dominated the phyllosphere, while Firmicutes exhibited increased relative abundance in the soil.

CONCLUSION: This study provides valuable insights into the microbial interactions associated with mango bacterial angular spot disease and highlights the role of soil fumigation in reshaping plant-associated microbiomes. The findings support the potential of fumigants in managing mango bacterial angular spot disease through microbial community regulation and offer a foundation for future research into microbial-based disease control strategies. © 2025 Society of Chemical Industry.},
}

@article {pmid41291883,
year = {2025},
author = {Anton, L and Cristancho, AG and Ferguson, B and Ravel, J and Elovitz, MA},
title = {Cervicovaginal microbiome alters transcriptomic and chromatin accessibility signatures across cervicovaginal epithelial barriers.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {238},
pmid = {41291883},
issn = {2049-2618},
support = {R01HD102318//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; 22-FY18-812//March of Dimes Foundation/ ; K08 NS119797/NS/NINDS NIH HHS/United States ; },
mesh = {Female ; Humans ; *Vagina/microbiology ; *Microbiota ; *Epithelial Cells/microbiology/metabolism ; *Chromatin/metabolism/genetics ; *Cervix Uteri/microbiology ; *Transcriptome ; Lactobacillus crispatus ; Host Microbial Interactions ; Gardnerella vaginalis ; },
abstract = {BACKGROUND: The cervicovaginal microbiome plays a critical role in women's health with microbial communities dominated by Lactobacillus species considered optimal. In contrast, the depletion of lactobacilli and the presence of a diverse array of strict and facultative anaerobes, such as Gardnerella vaginalis, have been linked with adverse reproductive outcomes. Despite these associations, the molecular mechanisms by which host-microbial interactions modulate cervical and vaginal epithelial function remains poorly understood.

RESULTS: In this study, we used RNA sequencing to characterize the transcriptional response of cervicovaginal epithelial cells exposed to the culture supernatants of common vaginal bacteria. Our findings revealed that G. vaginalis culture supernatants upregulate genes associated with an activated innate immune response and increased cell death. Conversely, Lactobacillus crispatus culture supernatants induced transcriptional changes indicative of epigenomic modeling in ectocervical epithelial cells. Epigenomic modification by L. crispatus was confirmed by ATAC-sequencing, which demonstrated reduced chromatin accessibility.

CONCLUSIONS: These results provide new insights into host-microbe interactions within the lower reproductive tract and suggest that modulating the cervicovaginal microbiome could offer innovative therapeutic strategies to improve reproductive health. Video Abstract.},
}

Female
Humans
*Vagina/microbiology
*Microbiota
*Epithelial Cells/microbiology/metabolism
*Chromatin/metabolism/genetics
*Cervix Uteri/microbiology
*Transcriptome
Lactobacillus crispatus
Host Microbial Interactions
Gardnerella vaginalis

@article {pmid41291881,
year = {2025},
author = {Binod, M and Chang, L and Hung, MW and Dong, TS and Kilpatrick, LA and Tomasevic, A and Choy, M and Shin, A and Mayer, EA and Church, A},
title = {Multi-omics analysis reveal clinical-gut-brain interactions in female ibs patients with adverse childhood experiences.},
journal = {Biology of sex differences},
volume = {16},
number = {1},
pages = {101},
pmid = {41291881},
issn = {2042-6410},
support = {T32DK007180/GF/NIH HHS/United States ; U54 DK123755/GF/NIH HHS/United States ; R01 MD015904/GF/NIH HHS/United States ; },
mesh = {Humans ; Female ; *Irritable Bowel Syndrome/physiopathology/microbiology/psychology/diagnostic imaging ; *Adverse Childhood Experiences ; *Gastrointestinal Microbiome ; Adult ; *Brain/diagnostic imaging/physiopathology ; Middle Aged ; *Brain-Gut Axis ; Magnetic Resonance Imaging ; Young Adult ; Multiomics ; },
abstract = {BACKGROUND: The brain-gut system, which involves bidirectional communication between the central nervous system and the gut, plays a central role in stress responses. Its dysregulation is implicated in irritable bowel syndrome (IBS), a stress-sensitive, female-predominant disorder characterized by abdominal pain and altered bowel habits. Adverse childhood experiences (ACE) increase the risk and severity of IBS, likely by amplifying stress responsiveness and gut-brain dysfunction in females. However, the mechanisms involved are unknown.

AIM: This study aimed to identify a multi-omic signature linking ACE exposure to IBS females via clinical, neuroimaging, and gut microbiome features as compared to healthy control (HC) females.

METHODS: Data was analyzed from participants with Rome positive IBS and HCs. Four subgroups were created based on IBS diagnosis and ACE score with high ACE defined as ≥2 and low as ACE 0-1. Validated questionnaires assessed clinical variables. Biological markers included multimodal brain MRI, and gut microbial function using metagenomics. eXtreme gradient boosting (XGBoost) identified key differentiating features between the groups. Connectograms visualized relationships across mutli-omics data within each group.

RESULTS: Among 188 female participants, the four groups included IBS with high ACE (n=37), IBS with low ACE (n=55), HCs with high ACE (n=19), and HCs with low ACE (n=77). Key findings include: 1. High ACE participants with IBS versus their HC counterparts showed increased depression and anxiety symptoms, GI-symptom related anxiety, perceived stress, somatic symptom severity, and poorer physical and mental health scores. 2. High ACE participants with IBS had negative associations between key bacteria such as Akkermansia (a beneficial bacteria) and somatic symptom severity, and between Bifidobacterium and ACE parental divorce/separation and alterations in the salience and central autonomic networks. 3. The ensemble model accurately distinguished IBS patients with high ACE (AUC of 0.87), demonstrating strong predictive performance with an overall model accuracy of 78%.

CONCLUSIONS: Our findings highlight the unique microbiota and brain networks contributing to a complex interplay of chronic stress as measured by early life adversity, the brain-gut-microbiome system, and IBS pathophysiology which can inform therapeutic targets aimed at mitigating the long-term impacts of early life stress in female IBS patients.},
}

Humans
Female
*Irritable Bowel Syndrome/physiopathology/microbiology/psychology/diagnostic imaging
*Adverse Childhood Experiences
*Gastrointestinal Microbiome
Adult
*Brain/diagnostic imaging/physiopathology
Middle Aged
*Brain-Gut Axis
Magnetic Resonance Imaging
Young Adult
Multiomics

@article {pmid41291759,
year = {2025},
author = {Azhdarimoghaddam, A and Mohammad Bigloo, A and Soleimani Meigoli, MS and Abdelbaset, M and Narimani, M and Dadkhah Tehrani, F and Asadi Anar, M and Abdolvand, F and Goudarzi, P and Ghazizadeh, Y and Mohammadzadeh, N and Eini, P and Khosravi, F and Abouzeid, M},
title = {Artificial intelligence at the gut-oral microbiota frontier: mapping machine learning tools for gastric cancer risk prediction.},
journal = {Biomedical engineering online},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12938-025-01487-1},
pmid = {41291759},
issn = {1475-925X},
abstract = {BACKGROUND: Gastric cancer (GC) remains a significant global health burden, with high mortality due to delayed diagnosis. Advances in microbiome profiling and artificial intelligence (AI) have opened new frontiers in non-invasive cancer risk prediction. However, the methodological landscape of AI-driven microbiome-based GC prediction remains fragmented and poorly standardized.

OBJECTIVE: To systematically review and critically evaluate artificial intelligence (AI) and machine learning (ML) models developed for gastric cancer prediction using microbial and non-invasive biomarkers, spanning gut, gastric mucosal, and oral ecosystems as well as tongue-based imaging proxies. We aimed to map methodological rigor, translational readiness, and biomarker convergence across these domains.

METHODS: We systematically searched PubMed, Scopus, and Web of Science for peer-reviewed studies published up to March 2025. Eligible studies applied ML or deep learning models to microbiome datasets for GC diagnosis, risk classification, or treatment response. Data extraction included sample source, sequencing method, taxonomic resolution, ML model type, validation strategy, performance metrics, interpretability tools, and reported microbial taxa. Descriptive synthesis, thematic clustering, and readiness scoring were conducted using structured visual analytics.

RESULTS: Nine studies met the inclusion criteria. Sample sources included gastric mucosa, feces, saliva, tongue coating, and tumor tissue. 16S rRNA sequencing was most common, with models primarily trained on genus-level data. Random Forest was the most frequently used algorithm (44.4%), followed by LASSO, LightGBM, and deep learning. AUC values ranged from 0.88 to 0.97 in validated models. However, only 33.3% of studies employed external validation, and interpretability and reporting standards varied widely. A Clinical Readiness Matrix and Validation Quality Assessment highlighted key translational gaps. Recurrent microbial biomarkers included Veillonella, Fusobacterium, Prevotella, and Porphyromonas.

CONCLUSION: AI-based microbiome models, including non-invasive diagnostics, show high potential for gastric cancer prediction. Yet, reproducibility, external validation, and reporting transparency remain critical barriers to clinical implementation. Standardized pipelines, multi-omics integration, and prospective validation are needed to transition this field from proof-of-concept to precision oncology.},
}

@article {pmid41291665,
year = {2025},
author = {Li, P and Wang, Z and Han, L and Geng, A and Zhao, X and Du, L and Yin, C and Sun, J and Shi, J and Fu, S and Guo, K and He, K},
title = {Metabolomic and microbiome integration of Han-Tibetan and plain-plateau populations.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {349},
pmid = {41291665},
issn = {1741-7007},
mesh = {Humans ; *Microbiota ; *Metabolome ; *Altitude ; Tibet ; Male ; Female ; Adult ; Bacteria/classification ; },
abstract = {BACKGROUND: Recent studies focus on the genetic and physiological characteristics of the plains Han, plateau Han, and Tibetan populations. However, systematic studies on the differences in metabolic and microbial communities in high-altitude environments remain limited.

RESULTS: This study profiled metabolomes and microbiomes in plain Han, plateau Han, and Tibetan populations. Differential analysis revealed 30 metabolites and notable alterations in microbial community composition between plain Han and plateau Han. Prevotella, Streptococcus, and Ruminococcus, mainly participating in purine metabolism, were enriched in the plateau Han population. Bacteroidota and Firmicutes were the primary differential bacterial phyla indicating adaptive alternatives, particularly in steroid metabolism. Thirty-four distinct metabolites were identified between plateau Han and Tibetan individuals, including significant lipids such as ceramide, triglycerides (TG), and phosphatidylethanolamine (PE). These lipids and metabolites were integrally involved in energy metabolism and inflammatory pathways, highlighting the importance of high-altitude environments for metabolic health.

CONCLUSIONS: This study identified significant associations between metabolic, lipid, and microbial differences and altitude-induced physiological variation, illustrating population adaptations to extreme environments. Our systematic comparative analysis improves our understanding of high-altitude adaptability, underlining the importance of integrating metabolic and microbiological analyses and facilitating future research on associated disorders.},
}

Humans
*Microbiota
*Metabolome
*Altitude
Tibet
Male
Female
Adult
Bacteria/classification

@article {pmid41291424,
year = {2025},
author = {Zhang, M and Wang, Y and Zhang, Q and Wang, H and Yan, Y},
title = {Identification of microbiome-associated loci in super hybrid rice reveals the regulation of OsBRI1 on nitrogen-dependent root microbiome assembly.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1634},
pmid = {41291424},
issn = {1471-2229},
support = {2022YFF1001800//National Key R&D Program of China/ ; XDA24020000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; },
mesh = {*Oryza/genetics/microbiology/metabolism ; *Plant Roots/microbiology/genetics/metabolism ; *Quantitative Trait Loci/genetics ; *Microbiota/genetics ; *Nitrogen/metabolism ; *Plant Proteins/genetics/metabolism ; Brassinosteroids ; },
abstract = {BACKGROUND: Host genetics is known to determine the composition of the plant microbiome, which plays an essential role in plant growth and nutrient use efficiency. Although an increasing number of candidate genetic loci controlling microbial selection have been identified through the population-level association studies in plants, only a few have been shown to shape microbiome assembly, and the genetic factors driving microbiome assembly remain largely elusive.

RESULTS: In this study, we use a segregating F2 population of LYP9, the widely cultivated super hybrid rice, to map root microbiome-associated loci by simultaneous whole genome resequencing and 16S rDNA amplicon sequencing. We identify 60 quantitative trait loci (QTLs) that correlate with the abundance of 43 ASVs of the root microbiome and reveal several microbiome-associated hotspot genomic regions. One such region is associated with different microbial taxa and contains 7 cytochrome P450 genes potentially involved in the brassinosteroid (BR) biosynthesis pathway. We further show that the miR444-overexpressing rice plants with increased BR biosynthesis alter the composition of the root microbiome and that the BR receptor OsBRI1 confers the distinction between nitrate- and ammonium-grown rice root microbiomes.

CONCLUSIONS: Using QTL analysis, our study identifies a set of genetic loci that link the root microbiome composition of the hybrid rice LYP9 and reveals that OsBRI1 regulates the assembly of the nitrogen-dependent rice root microbiome.},
}

*Oryza/genetics/microbiology/metabolism
*Plant Roots/microbiology/genetics/metabolism
*Quantitative Trait Loci/genetics
*Microbiota/genetics
*Nitrogen/metabolism
*Plant Proteins/genetics/metabolism
Brassinosteroids

@article {pmid41291258,
year = {2025},
author = {Eskiocak, O and Gewolb, J and Shah, V and Rouse, JA and Chowdhury, S and Akyildiz, EO and Fernández-Maestre, I and Boyer, JA and Filliol, A and Harris, AS and Utama, R and Guo, G and Castro-Hernández, C and Nnuji-John, E and Chung, C and Anderson, A and Flowers, S and Habel, J and Romesser, PB and Levine, RL and Lowe, SW and Sadelain, M and Beyaz, S and Amor, C},
title = {Anti-uPAR CAR T cells reverse and prevent aging-associated defects in intestinal regeneration and fitness.},
journal = {Nature aging},
volume = {},
number = {},
pages = {},
pmid = {41291258},
issn = {2662-8465},
abstract = {Intestinal stem cells (ISCs) drive the rapid regeneration of the gut epithelium. However, during aging, their regenerative capacity wanes, possibly through senescence and chronic inflammation, albeit little is known about how aging-associated dysfunction arises in the intestine. We previously identified the urokinase plasminogen activator receptor (uPAR) as a senescence-associated protein and developed CAR T cells able to efficiently target it. Harnessing them, here, we identify the accumulation of mostly epithelial uPAR-positive cells in the aging gut and uncover their detrimental impact on ISC function in aging. Thus, both therapeutic and prophylactic treatment with anti-uPAR CAR T cells improved barrier function, regenerative capacity, inflammation, mucosal immune function and microbiome composition in aged mice. Overall, these findings reveal the deleterious role of uPAR-positive cells on intestinal aging in vivo and provide proof of concept for the potential of targeted immune-based cell therapies to enhance tissue regeneration in aging organisms.},
}

@article {pmid41291224,
year = {2025},
author = {Khamsi, R},
title = {The ocular microbiome: more than meets the eye.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {41291224},
issn = {1476-4687},
}

@article {pmid41291164,
year = {2025},
author = {Shi, Z and Xiong, L and Li, Z and Shah, F and Yuan, Q and Whalen, JK and Wu, W},
title = {Biodegradable plastic exposure enhances microbial functional diversity while reducing taxonomic diversity across multi-kingdom soil microbiota in cherry tomato fields.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1675},
pmid = {41291164},
issn = {2399-3642},
support = {KYQD(ZR)20018//Hainan University (University of Hainan)/ ; },
mesh = {*Soil Microbiology ; *Solanum lycopersicum/growth & development/microbiology ; *Biodegradable Plastics ; *Microbiota/drug effects ; Biodiversity ; Bacteria/classification/drug effects/genetics ; Fungi/drug effects/classification/genetics ; Biodegradation, Environmental ; Soil/chemistry ; },
abstract = {Plastic films are extensively utilized in agroecosystems, and their residues are accumulating in global soil at a worrying rate. Biodegradable films are employed as a substitute for polyethylene (PE) films due to their rapid degradation rate. Although the taxonomic diversity of soil microbiome in response to biodegradable films has been studied, its alterations in functional diversity remain unexplored. Here, we conduct a two-year field experiment in cherry tomato to address how PE and poly (butylene adipate-co-terephthalate) (PBAT) influences soil microbiota across multi-kingdom (bacteria, fungi, and protists) regarding its taxonomic and functional diversity. The results show that PBAT exposure reduces the taxonomic diversity while increasing functional diversity across multi-kingdom domains compared to PE exposure. We further find that the decreased taxonomic diversity under PBAT exposure reduces the complexity of microbial inter-kingdom and internal-kingdom networks. Conversely, PBAT exposure enhances microbial functional diversity (Shannon index) and average genome size, accompanied by elevated abundances of plastic-degrading genes as well as carbon, nitrogen, phosphorus, and sulphur cycling functional genes. Overall, our study indicates that environmental filtration induced by PBAT exposure changes the microbial life adaptive strategies and leads to a decoupling between taxonomic diversity and functional diversity.},
}

*Soil Microbiology
*Solanum lycopersicum/growth & development/microbiology
*Biodegradable Plastics
*Microbiota/drug effects
Biodiversity
Bacteria/classification/drug effects/genetics
Fungi/drug effects/classification/genetics
Biodegradation, Environmental
Soil/chemistry

@article {pmid41291109,
year = {2025},
author = {Cohen, DD and Faigenboim, A and Elingold, I and Sher, Y and Galpaz, N and Minz, D},
title = {Dynamics in Microbial Communities Associated with the Development of Soil Fatigue in Banana.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02637-7},
pmid = {41291109},
issn = {1432-184X},
abstract = {Soil fatigue, well documented in various crops, presents a significant challenge to banana production by causing fast and then gradual declines in plant growth and yield over years of cultivation. Despite its impact on profitability, the underlying mechanisms driving soil fatigue remain poorly understood; however, a strong link to shifts in the soil microbiome has been suggested. We investigated the dynamics of microbial communities in relation to soil fatigue, using a novel semi-controlled outdoor experimental system. Soil at different stages of fatigue (0 to 42 months of banana cultivation) was generated in large containers filled with initially healthy soil. Banana plants grown in these soils were replaced with new plants which showed soil age-dependent growth. Three months postplanting, soil and root samples were collected for analyses of soil parameters and microbial community composition using bacterial (16S) and fungal (ITS) amplicon sequencing. We identified minor age-related shifts in mainly pH, potassium, and organic matter in the soil. While alpha diversity remained unchanged, significant shifts in bacterial and fungal community composition were observed in fatigued soils. Notably, the relative abundance of bacterial families such as Flavobacteriaceae, Pseudomonaceae, and Acidibacter increased, as did some fungal taxa (many from groups with known pathogens)-Ceratobasidiaceae (including Rhizoctonia), Dothideomycetes, and Stachybotryaceae. Simultaneously, the relative abundance of bacterial families with known beneficial members, including Gemmatimonadaceae, Moraxellaceae, Sphingomonadaceae, and Azospirillaceae, as well as symbiotic fungal taxa such as Glomeraceae and Lasiosphaeriaceae, declined. Thus, soil fatigue may be correlated to the proliferation of pathogenic populations and a loss of beneficial microorganisms.},
}

@article {pmid41290854,
year = {2025},
author = {Chauhan, A and Chukwujindu, C and Pathak, A and Jaswal, R},
title = {A survey of bacterial and fungal community structure and functions in two long-term metalliferous soil habitats.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {41955},
pmid = {41290854},
issn = {2045-2322},
mesh = {*Soil Microbiology ; *Bacteria/genetics/classification ; *Fungi/genetics/classification ; *Soil Pollutants/analysis ; Mercury/analysis ; Ecosystem ; *Microbiota ; Soil/chemistry ; Metagenomics ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Mercury contamination at legacy nuclear sites such as the Savannah River Site and Oak Ridge Reservation poses persistent ecological risks, yet its impact on soil microbiomes remains incompletely understood. This study integrates qPCR, 16S/ITS amplicon sequencing, and shotgun metagenomics to assess bacterial and fungal community structure, diversity, and functional potential across gradients of total mercury, methylmercury, and bioavailable mercury. Bacterial α-diversity declined with increasing Hg levels, while fungal diversity remained stable and highest in low-contamination soils. Dominant bacterial phyla included Pseudomonadota, Bacteroidota, Bacillota, Acidobacteriota, and Actinomycetota; fungal communities were primarily Ascomycota and Basidiomycota. Canonical correspondence analysis revealed distinct taxon-Hg speciation linkages, and functional gene profiling showed enrichment of stress-response genes, membrane transporters, and phosphate metabolism pathways in contaminated soils. Notably, bioavailable Hg did not correlate directly with total Hg, underscoring the importance of speciation in microbial exposure. These findings highlight the adaptive plasticity of native microbiomes and identify microbial taxa and pathways relevant to bioremediation and can guide ecosystem restoration activities in Hg-impacted soil habitats.},
}

*Soil Microbiology
*Bacteria/genetics/classification
*Fungi/genetics/classification
*Soil Pollutants/analysis
Mercury/analysis
Ecosystem
*Microbiota
Soil/chemistry
Metagenomics
Biodiversity
RNA, Ribosomal, 16S/genetics

@article {pmid41290836,
year = {2025},
author = {Brito, LFC and Althouse, GC and Pitta, DW and Indugu, N and Sarmiento, MP and Balamurugan, NS},
title = {Temporal dynamics of the resistome in gilts raised in an organic operation in which semen used for artificial insemination is the primary source of antimicrobial exposure.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {41935},
pmid = {41290836},
issn = {2045-2322},
mesh = {Animals ; *Insemination, Artificial/veterinary/methods ; *Semen/microbiology ; Swine ; Female ; Male ; Feces/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Microbiota/drug effects ; Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Metagenomics ; },
abstract = {Natural bacterial contaminants in boar semen make it necessary to use preservative-level antibiotics in semen extenders to ensure long-term sperm viability and artificial insemination (AI) success. While concerns exist about the role of semen extender antibiotics in antimicrobial resistance (AMR), empirical evidence is lacking. This study examined microbiome and resistome dynamics in fecal samples of gilts from an organic farming operation, where AI is the primary source of antimicrobial exposure. Metagenomics was used to analyze microbial communities and antibiotic resistance genes (ARGs) across quarantine, breeding pen introduction, and post-AI production phases. The fecal microbiome was dominated by Bacillota and Bacteroidota. Microbial shifts were likely due to environmental and dietary adaptation, with no major changes observed post-AI. Among 168 identified ARGs, 89% were linked to drug resistance, primarily targeting tetracyclines, aminoglycosides, and macrolides, lincosamides and streptogramins (MLS). The abundance of most ARGs decreased between arrival at the operation and 10 days after introduction into the breeding pen, with no major resistome changes post-AI. Neither exposure to previously inseminated females nor antibiotics in semen extenders increased fecal ARGs. This study found no evidence that rational antibiotic use in swine semen extender contributes to increased antimicrobial resistance in the swine fecal microbiome.},
}

Animals
*Insemination, Artificial/veterinary/methods
*Semen/microbiology
Swine
Female
Male
Feces/microbiology
*Anti-Bacterial Agents/pharmacology
*Microbiota/drug effects
Bacteria/genetics/drug effects
*Drug Resistance, Bacterial/genetics
*Drug Resistance, Microbial/genetics
Metagenomics

@article {pmid41290820,
year = {2025},
author = {Silvestre, AM and Squizatti, MM and Felizari, LD and Demartini, BL and Silva, LAF and Casali, DM and Souza, JM and Virgínio, GF and Suen, G and Millen, DD},
title = {Nutritional protocols that shift ruminal microbiota to improve the feedlot performance of Nellore cattle differing in marbling EPD.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {41785},
pmid = {41290820},
issn = {2045-2322},
support = {2019/24747-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2019/20164-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; },
mesh = {Animals ; Cattle ; *Rumen/microbiology ; *Animal Feed/analysis ; Male ; Diet/veterinary ; Dietary Supplements ; *Gastrointestinal Microbiome ; *Animal Nutritional Physiological Phenomena ; Zea mays ; },
abstract = {This study evaluated the effects of high-moisture corn (HMC), rumen-protected fat (CSFA), and organic zinc plus chromium (ZnCr) supplementation, alone or in combination, on feedlot performance, rumen microbiota, carcass traits, and feeding behavior of Nellore cattle with divergent marbling EPD. A total of 150 Nellore yearling bulls were classified into high and low EPD groups and assigned to five diets: (1) fine ground corn (FGC); (2) high-moisture corn (HMC); (3) FGC + calcium salts of fatty acids (FGC + CSFA); (4) HMC + CSFA; and (5) HMC + CSFA + ZnCr (organic zinc and chromium added). The HMC improved average daily gain and gain-to-feed ratio while reducing dry matter intake. The CSFA inclusion enhanced carcass traits and reduced incidence of rumenitis, improving rumen health. The ZnCr supplementation increased glucose availability and dressing percentage, especially in high-EPD animals. Genetic predisposition for marbling influenced dietary responses, with high-EPD bulls showing greater fat deposition and energy efficiency. Rumen microbiota composition was altered by corn processing, CSFA, and ZnCr, particularly affecting specific taxa such as Prevotella, Butyrivibrio, and Firmicutes. Feeding behavior and ruminal morphometry also varied with diet and genetic group. In conclusion, it is recommended to combine HMC and CSFA, while ZnCr proves to be most effective in marbling-genetically predisposed cattle.},
}

Animals
Cattle
*Rumen/microbiology
*Animal Feed/analysis
Male
Diet/veterinary
Dietary Supplements
*Gastrointestinal Microbiome
*Animal Nutritional Physiological Phenomena
Zea mays

@article {pmid41290754,
year = {2025},
author = {Hio, M and Murata, K and Takase, R and Ogura, K and Hashimoto, W},
title = {Spontaneous fermentation of raisin water to form wine.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {39194},
pmid = {41290754},
issn = {2045-2322},
mesh = {*Wine/microbiology/analysis ; *Fermentation ; *Vitis/microbiology ; Water ; Microbiota ; },
abstract = {Yeast obtained from the water containing raisins has been conventionally used for breadmaking. It is assumed that people consumed naturally fermented raisin water as wine in ancient times. In this study, we demonstrated spontaneous fermentation by yeast that colonizes raisins. Raisin water samples containing Saccharomyces and non-Saccharomyces species underwent alcohol fermentation. As the fermentation progressed, the diversity and abundance of Aspergillus decreased. A significant difference in β diversity was detected between the microbiomes of raw grapes and raisins, with raisins containing a higher ratio of Saccharomycetaceae. The yeast colonizing raisin fermented alcohol more efficiently than those on raw grapes. Outdoor-dried raisins harbored a distinct eukaryotic microbiome that successfully fermented alcohol, indicating that these yeasts migrate from the environment. Therefore, our data suggest that sun-drying grapes can be utilized for food preservation and making alcoholic beverages, validating the ancient practice of wine-making from raisins due to spontaneous fermentation.},
}

*Wine/microbiology/analysis
*Fermentation
*Vitis/microbiology
Water
Microbiota

@article {pmid41290716,
year = {2025},
author = {Caesar, L and Barksdale, C and Valiati, VH and Newton, I},
title = {Spatial segregation and cross-kingdom interactions drive stingless bee hive microbiome assembly.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66678-9},
pmid = {41290716},
issn = {2041-1723},
support = {2022049//National Science Foundation (NSF)/ ; 2005306//National Science Foundation (NSF)/ ; },
abstract = {Studying host-associated microbiome assembly is key to understanding microbial and host evolution and health. While honey bee microbiome have been a central model for such investigations among pollinators, they overlook the diversity of eusocial dynamics and multi-kingdom interactions. Stingless bees-a diverse group of highly eusocial insects that includes managed species, varies in colony biology, and harbors a symbiotic yeast essential for larval development in at least one species-offer a valuable complementary system to study microbiome assembly under an eco-evolutionary context. Using amplicon sequencing, metagenomics, and microbial experiments, we investigate the drivers of microbiome assembly in stingless bee colonies. We reveal a spatially structured, site-adapted microbiome, where high microbial influx hive components are segregated from the brood, which harbors a stable, multi-kingdom community. We show that the brood microbiome is not only physically protected but also maintained through selective bacterial-fungal interactions and abiotic conditions shaped by bees and their symbionts, such as temperature and pH. Our findings uncover multi-layered mechanisms shaping eusocial superorganism microbiomes, from host biology to cross-kingdom interactions, while providing critical insights into microbiome maintenance of important pollinators.},
}

@article {pmid41290715,
year = {2025},
author = {Zhang, S and Shoaie, S and Carpenter, GH},
title = {L-proline supplementation affects non-volatile flavour perception through oral microbiome metabolic pathways.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-025-00643-0},
pmid = {41290715},
issn = {2396-8370},
abstract = {L-proline is a non-essential amino acid that can be metabolised by the oral microbiome. This study hypothesised that L-proline could influence the microbiome and that shifts in the microbiome could subsequently affect non-volatile flavour perception. A semi-trained panel (n = 20) completed sensory assessments using the generalised labelled visual analogue scale (glVAS) for nine tastants at baseline, during a five-day supplementation phase, and post-supplementation within a three-week protocol. Analysis at the tastant level identified a significant increase in menthol taste perception (p = 0.011, Wilcoxon) during supplementation at the group level (n = 20). Shotgun sequencing results demonstrated a distinct beta diversity separation in metabolic pathways during supplementation at the entire group level (p = 0.008). Piano analysis suggested that increased protein synthesis could influence non-volatile flavour perception, while lipopolysaccharide (LPS) might prevent changes in non-volatile flavour perception via immune response. A mixed-effects linear regression model revealed that metabolic pathways were stronger predictors of non-volatile flavour perception than the microbiome itself. The metabolic pathways were positively associated with menthol taste and sodium chloride perception. In conclusion, L-proline supplementation affected metabolic pathways, which altered non-volatile flavour perception.},
}

@article {pmid41279261,
year = {2025},
author = {Schuran, FA and Mishra, N and López-Agudelo, VA and Sommer, N and Bernardes, JP and Walker, A and Hinrichsen, F and Gong, T and Gilbert, F and Schröder, L and Bhardwaj, A and Künzel, S and Weber-Stiehl, S and Ito, G and Tran, F and Groussin, M and Röcken, C and Matute, J and Schreiber, S and Penninger, JM and Blumberg, RS and Schmitt-Kopplin, P and Baines, JF and Sommer, F and Rosenstiel, P},
title = {Long-Term Intestinal Epithelial Remodeling Induced by Acute Protein-Energy Malnutrition.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41279261},
issn = {2692-8205},
abstract = {Protein-energy malnutrition (PEM) is a global health burden with lasting effects that extend well beyond the initial nutrient deficiency. To systematically investigate the long-term effects of a single episode of PEM on the structure and function of the intestinal epithelium and its associated microbiota, we employed a comprehensive multi-omics approach, including (spatial) transcriptomics, DNA methylation analysis, fecal metagenomics, and metabolomics. Our findings show that PEM persistently alters the intestinal epithelium by depleting Paneth cells and suppressing antimicrobial gene expression - changes linked to DNA methylation that persist despite dietary recovery. In germ-free mice, the sustained epithelial phenotype after was absent. We identified the microbial lipid metabolite 9-HODE and epigenetically deregulated PPAR-driven GDF15 expression as key molecular drivers of the persistent PEM-induced Paneth cell dysfunction. Targeting microbial lipid production and its link to the host GDF15 pathway could offer novel therapeutic strategies for long-term consequences of malnutrition and other Paneth cell-associated diseases.},
}

@article {pmid41290697,
year = {2025},
author = {Huang, Y and Zhao, X and Cai, M and Xia, Z and Li, B and Yu, J and Sheng, Q and Tang, Q and Gao, Q and Yi, S},
title = {A metabolome and microbiome dataset of male morphotype differentiation in giant freshwater prawn Macrobrachium rosenbergii.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1866},
pmid = {41290697},
issn = {2052-4463},
mesh = {Animals ; *Palaemonidae/microbiology/metabolism/growth & development/anatomy & histology ; Male ; *Metabolome ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; Hemolymph/metabolism ; *Microbiota ; Phenotype ; },
abstract = {This integrated multi-omics resource delineates the molecular and phenotypic trajectories underlying male morphotype differentiation (Blue Claw [BC], Orange Claw [OC], Small Male [SM]) in Macrobrachium rosenbergii during determinative developmental stages (100, 110, and 120 days post-stocking). The dataset comprises hemolymph metabolomes, gut microbiota 16S rRNA sequencing data and quantitative morphological trait data, thereby establishing a holistic framework capturing metabolic flux alterations, microbial community structure and phenotypic manifestations throughout morphotype specification. The synergistic integration of these layers provides support for the identification of heritable biomarkers linked to commercially advantageous morphotypes and reveals the important role of host-microbiota interactions in phenotypic divergence. All raw and processed omics data are deposited in NCBI SRA and Metabolights.},
}

Animals
*Palaemonidae/microbiology/metabolism/growth & development/anatomy & histology
Male
*Metabolome
RNA, Ribosomal, 16S/genetics
*Gastrointestinal Microbiome
Hemolymph/metabolism
*Microbiota
Phenotype

@article {pmid41290541,
year = {2025},
author = {Zhang, J and Zhou, M and Xie, Y},
title = {A microbiome-epigenome axis: SRB-derived H2S suppresses OsHDA710 to activate drought responses in rice.},
journal = {Journal of integrative plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jipb.70104},
pmid = {41290541},
issn = {1744-7909},
support = {BK20220084//Jiangsu Natural Science Foundation for Distinguished Young Scholars./ ; },
abstract = {This commentary highlights the recent identification of exogenous application of sodium butyrate, as a histone deacetylase inhibitor that improves rice drought resistance via enriching sulfate-reducing bacteria to elevate rhizosphere-derived H2S production, which in turn represses OsHDA710 expression and activity to activate drought responses.},
}

@article {pmid41290520,
year = {2025},
author = {Kumari, A and Priya, S and Barman, I and Dhasmana, A and Rustagi, S and Thapliyal, S and Deshwal, RK and Malik, S and Bora, J},
title = {Gut Microbiota Dynamics and Their Role in Pathogenesis and Management of Diabetes.},
journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica},
volume = {133},
number = {11},
pages = {e70090},
doi = {10.1111/apm.70090},
pmid = {41290520},
issn = {1600-0463},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Diabetes Mellitus, Type 2/microbiology/therapy ; Dysbiosis/microbiology ; *Diabetes Mellitus, Type 1/microbiology/therapy ; Fecal Microbiota Transplantation ; Animals ; Probiotics/therapeutic use ; Prebiotics ; },
abstract = {The gut microbiota (GM) has emerged as an important element in the management of host metabolism, immune functions, and overall metabolic well-being. This review consolidates contemporary research regarding the intricate relationship between GM and diabetes mellitus, focusing on the mechanisms by which microbial composition and activity affect the development of both Type 1 (T1D) and Type 2 diabetes (T2D). Dysbiosis-characterized by diminished microbial diversity, a modified Firmicutes/Bacteroidetes ratio, and a reduction in advantageous SCFA-producing bacteria-has been significantly associated with disrupted glucose metabolism, insulin resistance, and persistent inflammation. Additionally, the review discusses the potential for microbial signatures and metabolites, such as SCFAs, lipopolysaccharides (LPS), and trimethylamine N-oxide (TMAO), to serve as novel biomarkers for early detection and risk evaluation. Moreover, it investigates therapeutic approaches designed to reestablish microbial balance through the use of probiotics, prebiotics, dietary changes, fecal microbiota transplantation (FMT), and microbiome engineering. By integrating findings from recent research, this paper emphasizes the groundbreaking possibilities of microbiome-centric diagnostics and treatments in individualized diabetes care.},
}

Humans
*Gastrointestinal Microbiome
*Diabetes Mellitus, Type 2/microbiology/therapy
Dysbiosis/microbiology
*Diabetes Mellitus, Type 1/microbiology/therapy
Fecal Microbiota Transplantation
Animals
Probiotics/therapeutic use
Prebiotics

@article {pmid41289893,
year = {2025},
author = {Francisco, R and Hernandez, SM and Aguirre, JI and López-García, A and Sacristán, I and Martín-Maldonado, B and Lattner, SP and Norfolk, WA and Perez, KM and Reyes, JR and Esperón, F},
title = {Exploring the diversity and burden of antimicrobial resistance genes carried by white stork (Ciconia ciconia) throughout the breeding season in Madrid, Spain.},
journal = {The Science of the total environment},
volume = {1008},
number = {},
pages = {180986},
doi = {10.1016/j.scitotenv.2025.180986},
pmid = {41289893},
issn = {1879-1026},
abstract = {Anthropogenic environments are critical hotspots for the emergence and persistence of antimicrobial resistance (AMR). Extensive livestock pastures and landfills are of particular concern due to their high bacterial diversity and frequent wildlife visitation, facilitating the transfer of antimicrobial resistance genes (ARGs). The white stork (Ciconia ciconia) heavily exploits landfills and extensive pastures in Spain, providing an ideal model to study AMR emergence. We evaluated the diversity and burden of ARGs in breeding white storks across three stages of the breeding season, reflecting different foraging strategies. Fecal samples from 31 nests were collected during two breeding seasons (2020-2021) and screened for 21 ARGs across eight antibiotic classes using real-time qPCR. ARGs were universally present, and over 70 % of nests contained fecal samples harboring genes conferring resistance to three or more antibiotic classes, indicating a high burden of potential multi-drug resistance at the community level. Generalized linear models identified breeder age and sampling period as strong predictors of total ARG burden (p < 0.001), with older breeders contributing more ARG burden early in the season, although this effect diminished later. Landfill use showed only a weak association with ARG burden, while nest success approached significance. These findings suggest that foraging dynamics, rather than landfill exposure alone, strongly influence ARG acquisition in white storks. Agricultural pastures and other anthropogenic environments may play a larger role in shaping resistomes than previously assumed. Understanding how wildlife foraging behavior drives AMR carriage is crucial to better characterize AMR transmission risk at the wildlife-livestock interface.},
}

@article {pmid41289425,
year = {2025},
author = {},
title = {Studies Challenge Cancer-Microbiome Links.},
journal = {Cancer discovery},
volume = {},
number = {},
pages = {OF1},
doi = {10.1158/2159-8290.CD-NW2025-0104},
pmid = {41289425},
issn = {2159-8290},
abstract = {Two recent studies analyzing cancer genome data suggest that microbial DNA is not a common feature across most tumors, challenging earlier suggestions of a pan-cancer microbiome. Colorectal cancer stands as an exception, with one study providing strong evidence of a microbial signature. Oral cancer may also be an exception. Both studies point to contamination as a key driver of false signals.},
}