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Duran C, Dupuy C, Agogué H, Duran R, Cravo-Laureau C. Towards a comprehensive view of wetland benthic communities. CURRENT RESEARCH IN MICROBIAL SCIENCES 2025; 8:100391. [PMID: 40321238 PMCID: PMC12048814 DOI: 10.1016/j.crmicr.2025.100391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2025] Open
Abstract
Benthic prokaryotic communities, utmost important for wetlands and marine environments functioning, are influenced by physical-chemical parameters and interactions with other communities, especially micro-eukaryotes and meiofauna. Thus, a holistic view of the benthic community is necessary to fully understand their organization and functioning. This study assesses the implementation of a comprehensive view, using mock communities and environmental samples. A DNA extraction strategy combining two procedures is proposed: one to obtain DNA from micro-organisms, using 0.25 g of sediment, and the other from meiofauna, using 0.25 g of sieving refluxes from 5 g of sediment. Three conditions were considered to create mock communities: (i) varying eukaryotes' abundance, (ii) adding meiofauna from salted or freshwater wetlands, and (iii) including or not a sediment matrix. Most organisms composing the mock communities were detected, except a filamentous cyanobacteria. All mock communities showed similar composition indicating that sediment did not affect the DNA extraction. This result also demonstrated that sieving, necessary to enrich meiofauna from sediment, does not significantly affect any of the communities. For the environmental samples investigated, most of the taxa usually described in the literature were retrieved in the salted, brackish and freshwater marshes sediment. The proposed approach was successful in analysing organisms from the three domains of life in a unique environmental sample, providing a holistic view of the benthic community. Furthermore, the significant differences observed between samples from the three different marshes, indicated that our approach can be used for conducting successful ecological studies, especially useful for understanding benthic communities' interactions.
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Affiliation(s)
- Clélia Duran
- Universite de Pau et des Pays de l'Adour, UPPA, CNRS, IPREM, Pau, France
- UMR 7266 LIENSs (Littoral Environnement et Sociétés), CNRS - La Rochelle Université, La Rochelle, France
| | - Christine Dupuy
- UMR 7266 LIENSs (Littoral Environnement et Sociétés), CNRS - La Rochelle Université, La Rochelle, France
| | - Hélène Agogué
- UMR 7266 LIENSs (Littoral Environnement et Sociétés), CNRS - La Rochelle Université, La Rochelle, France
| | - Robert Duran
- Universite de Pau et des Pays de l'Adour, UPPA, CNRS, IPREM, Pau, France
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Bentanachs R, Miró L, Ramírez-Carrasco P, Sánchez RM, Bernabeu M, Amat C, Alegret M, Pérez-Bosque A, Roglans N, Laguna JC. Mirabegron induces selective changes in the faecal microbiota of HFHFr rats without altering bile acid composition. Front Pharmacol 2025; 16:1547749. [PMID: 40297137 PMCID: PMC12034709 DOI: 10.3389/fphar.2025.1547749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2024] [Accepted: 03/27/2025] [Indexed: 04/30/2025] Open
Abstract
Introduction Metabolic dysfunction-associated steatotic liver (MASL), the initial, asymptomatic stage of the metabolic dysfunction-associated steatotic liver disease, is directly involved in the progression to steatohepatitis. Healthy lifestyle and dietary measures are currently the only treatments for MASL. Given the high prevalence of MASL in the human population, candidate drugs for its prevention or treatment should have an acceptable safety profile. Repurposing drugs already in clinical use could help to identify effective and safe drug treatments for MASL. We have characterized a high-fat, high-fructose rat dietary model of simple hepatic steatosis to evaluate the potential anti-steatotic effect of mirabegron, which is already in clinical use for the treatment of overactive bladder. We have previously reported that mirabegron administration was unable to reduce liver triglyceride content in our rat model. Methods In the present work, we analyse stored liver, adipose tissue (perigonadal and brown), serum and faecal samples from our previous study and present new biochemical, faecal metabolomic and microbiome data. Results and discussion We show that oral administration of mirabegron significantly increases the expression of uncoupling protein 1 in brown adipose tissue and β3-Adrenergic receptor protein in perigonadal white adipose and liver tissues. Furthermore, mirabegron treatment changes the relative abundance of several genus and families of rat faecal microbiota, albeit without restoring the global biodiversity and evenness indexes observed in control rats, as well as faecal bile acids composition. These changes are probably due to a direct effect of mirabegron on the gut microbiome, rather than being mediated by changes in bile acid induced by drug treatment.
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Affiliation(s)
- Roger Bentanachs
- Department of Pharmacology, Toxicology and Therapeutic Chemistry, School of Pharmacy and Food Science, University of Barcelona, Barcelona, Spain
- Institute of Biomedicine IBUB, University of Barcelona, Barcelona, Spain
| | - Lluïsa Miró
- Department of Biochemistry and Physiology, School of Pharmacy and Food Science, University of Barcelona, Barcelona, Spain
- Institute for Nutrition and Food Safety Research INSA-UB, University of Barcelona, Barcelona, Spain
| | - Patricia Ramírez-Carrasco
- Department of Pharmacology, Toxicology and Therapeutic Chemistry, School of Pharmacy and Food Science, University of Barcelona, Barcelona, Spain
| | - Rosa M. Sánchez
- Department of Pharmacology, Toxicology and Therapeutic Chemistry, School of Pharmacy and Food Science, University of Barcelona, Barcelona, Spain
- Institute of Biomedicine IBUB, University of Barcelona, Barcelona, Spain
- Spanish Biomedical Research Centre in Physiopathology of Obesity and Nutrition (CIBEROBN), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Manuel Bernabeu
- Department of Biotechnology, Institute of Agrochemistry and Food Technology, National Research Council (IATA-CSIC), Paterna, Spain
| | - Concepció Amat
- Department of Biochemistry and Physiology, School of Pharmacy and Food Science, University of Barcelona, Barcelona, Spain
- Institute for Nutrition and Food Safety Research INSA-UB, University of Barcelona, Barcelona, Spain
| | - Marta Alegret
- Department of Pharmacology, Toxicology and Therapeutic Chemistry, School of Pharmacy and Food Science, University of Barcelona, Barcelona, Spain
- Institute of Biomedicine IBUB, University of Barcelona, Barcelona, Spain
- Spanish Biomedical Research Centre in Physiopathology of Obesity and Nutrition (CIBEROBN), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Anna Pérez-Bosque
- Department of Biochemistry and Physiology, School of Pharmacy and Food Science, University of Barcelona, Barcelona, Spain
- Institute for Nutrition and Food Safety Research INSA-UB, University of Barcelona, Barcelona, Spain
| | - Núria Roglans
- Department of Pharmacology, Toxicology and Therapeutic Chemistry, School of Pharmacy and Food Science, University of Barcelona, Barcelona, Spain
- Institute of Biomedicine IBUB, University of Barcelona, Barcelona, Spain
- Spanish Biomedical Research Centre in Physiopathology of Obesity and Nutrition (CIBEROBN), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Juan C. Laguna
- Department of Pharmacology, Toxicology and Therapeutic Chemistry, School of Pharmacy and Food Science, University of Barcelona, Barcelona, Spain
- Institute of Biomedicine IBUB, University of Barcelona, Barcelona, Spain
- Spanish Biomedical Research Centre in Physiopathology of Obesity and Nutrition (CIBEROBN), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
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103
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Huttunen KL, Malazarte J, Jyväsjärvi J, Lehosmaa K, Muotka T. Temporal Beta Diversity of Bacteria in Streams: Network Position Matters But Differently for Bacterioplankton and Biofilm Communities. MICROBIAL ECOLOGY 2025; 88:26. [PMID: 40216640 PMCID: PMC11992004 DOI: 10.1007/s00248-025-02522-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2025] [Accepted: 03/31/2025] [Indexed: 04/14/2025]
Abstract
Concern about biodiversity loss has yielded a surge of studies on temporal change in α-diversity, whereas temporal β-diversity has gained less interest. We sampled bacterioplankton, biofilm, and riparian soil bacteria repeatedly across the open-water season in a pristine stream network to determine the level of temporal β-diversity in relation to stream network position and environmental variability. We tested the hypothesis that aquatic bacterial communities in isolated and environmentally heterogenous headwaters exhibit high temporal β-diversity while the better-connected and environmentally more stable mainstem sections support more stable communities, and soil communities bear no relationship to network position. As expected, temporal β-diversity decreased from headwaters toward mainstems for bacterioplankton. Against expectations, an opposite pattern was observed for biofilm. For bacterioplankton, temporal β-diversity was positively related to temporal variability in water chemistry. For biofilm bacteria, temporal variability was negatively related to variability in temperature. Temporal β-diversity of soil communities did not show any response to stream network position, but was strongly related to variability in the soil environment. The two aquatic habitats and riparian soils supported distinctly different bacterial communities. The number of ASVs shared between the soil and the aquatic communities decreased along the network, and more so for bacterioplankton. The higher temporal variability of bacterial communities in the headwaters likely results from temporally variable input of propagules from riparian soil, emphasizing the role of land-water connection and network position to bacterioplankton community composition. Overall, bacterial communities exhibited high temporal variability, highlighting the importance of temporal replication to fully capture their network-scale biodiversity.
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Affiliation(s)
- Kaisa-Leena Huttunen
- Finnish Environment Institute, Nature Solutions Unit, Oulu, Finland.
- University of Oulu, Ecology and Genetics Research Unit, Oulu, Finland.
| | - Jacqueline Malazarte
- University of Oulu, Water, Energy, and Environmental Engineering Research Unit, Oulu, Finland
| | - Jussi Jyväsjärvi
- University of Oulu, Ecology and Genetics Research Unit, Oulu, Finland
- Centre for Economic Development, Transport and the Environment of North Ostrobothnia, Oulu, Finland
| | - Kaisa Lehosmaa
- University of Oulu, Ecology and Genetics Research Unit, Oulu, Finland
| | - Timo Muotka
- University of Oulu, Oulanka Research Station, Kuusamo, Finland
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Brinkerhoff RJ, Pandian J, Leber M, Hauser ID, Gaff HD. Impacts of Tick Parasitism on the Rodent Gut Microbiome. Microorganisms 2025; 13:888. [PMID: 40284724 PMCID: PMC12029286 DOI: 10.3390/microorganisms13040888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2025] [Revised: 03/06/2025] [Accepted: 04/08/2025] [Indexed: 04/29/2025] Open
Abstract
Host microbiota may impact disease vector behavior and pathogen transmission, but little is known about associations between ectoparasites and microbial communities in wildlife reservoir species. We used Illumina metagenomic sequencing to explore the impacts of tick parasitism on the rodent fecal microbiome in both a field and laboratory setting. We found that tick parasitism on wild hosts was associated with variation in the fecal microbiota of both the white-footed deermouse, Peromyscus leucopus, and the southern cotton rat, Sigmodon hispidus. In a lab experiment, we detected significant changes to the fecal microbiome after experimental exposure to immature ticks in treated versus control BALB/c mice. Whereas there is variation in the fecal microbiome associated with each of the host species we tested, some of the same microbial taxa, notably members of the family Muribaculaceae, occurred at higher relative abundance in tick-parasitized hosts in both the field and laboratory studies, suggesting that there are consistent impacts of tick parasitism on the host gut microbiome. We recommend future studies to test the hypothesis that epithelial cell secretions, generated as part of the host's immune response to tick parasitism, could provide resources that allow particular microbial lineages in the mammalian gut to flourish.
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Affiliation(s)
| | - Joshua Pandian
- Biology Department, University of Richmond, Richmond, VA 23173, USA (I.D.H.)
| | - Meghan Leber
- Biology Department, University of Richmond, Richmond, VA 23173, USA (I.D.H.)
| | - Isabella D. Hauser
- Biology Department, University of Richmond, Richmond, VA 23173, USA (I.D.H.)
| | - Holly D. Gaff
- Biology Department, Old Dominion University, Norfolk, VA 23529, USA
- School of Mathematics and Computer Science, University of KwaZulu-Natal, Durban 4041, South Africa
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105
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Knoppersen RS, Bose T, Coutinho TA, Hammerbacher A. Inside the Belly of the Beast: Exploring the Gut Bacterial Diversity of Gonipterus sp. n. 2. MICROBIAL ECOLOGY 2025; 88:27. [PMID: 40220189 PMCID: PMC11993490 DOI: 10.1007/s00248-025-02524-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2025] [Accepted: 04/02/2025] [Indexed: 04/14/2025]
Abstract
The Eucalyptus snout beetle (Gonipterus sp. n. 2) is a destructive invasive pest of Eucalyptus plantations, responsible for significant defoliation and wood yield losses globally. Native to Australia, this beetle has adapted to thrive on diverse Eucalyptus hosts, overcoming their chemical defences. However, the mechanisms by which Gonipterus tolerates or utilises these plant defence metabolites remain poorly understood. In South Africa, Gonipterus sp. n. 2 poses a significant threat to Eucalyptus plantations by causing extensive defoliation and leading to substantial reductions in growth and wood production. This study investigates the relationship between diet, host Eucalyptus species, and the gut microbiome of Gonipterus sp. n. 2. Using controlled feeding experiments, beetles were reared on artificial, semi-artificial, and natural diets, as well as two Eucalyptus genotypes with distinct secondary metabolite profiles. High-throughput 16S rDNA sequencing and gas chromatography-mass spectrometry (GC-MS) revealed significant shifts in gut bacterial diversity and composition across diets. Natural diets supported the most diverse microbial communities, while artificial diets fostered a homogenised microbiome dominated by opportunistic taxa like Serratia. Host-specific effects were observed in frass microbiota, with substantial biotransformation of monoterpenes into less toxic derivatives. The results highlight the plasticity of Gonipterus gut microbiota, which enables metabolic adaptability and resilience in diverse environments. This microbial flexibility underpins the invasiveness of Gonipterus, emphasising the role of gut symbionts in overcoming host chemical defences. Understanding these interactions offers novel insights for microbiome-targeted pest management strategies, providing a sustainable approach to mitigate the impact of Gonipterus on global Eucalyptus forestry.
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Affiliation(s)
- Rosa S Knoppersen
- Department of Zoology and Entomology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Tanay Bose
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa.
| | - Teresa A Coutinho
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
- Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, 0002, South Africa
| | - Almuth Hammerbacher
- Department of Zoology and Entomology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa.
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Wu X, Liao H, Zhang X, Ma Z, Fu Z. Unraveling the Impact of Microplastic-Tetracycline Composite Pollution on the Moon Jellyfish Aurelia aurita: Insights from Its Microbiome. Microorganisms 2025; 13:882. [PMID: 40284718 PMCID: PMC12029949 DOI: 10.3390/microorganisms13040882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2025] [Revised: 04/04/2025] [Accepted: 04/09/2025] [Indexed: 04/29/2025] Open
Abstract
Microplastics have emerged as a pervasive marine contaminant, with extreme concentrations reported in deep-sea sediments (e.g., 1.9 million particles/m2) and localized accumulations near Antarctic research stations. Particular concern has been raised regarding their synergistic effects with co-occurring antibiotics, which may potentiate toxicity and facilitate antibiotic resistance gene dissemination through microbial colonization of plastic surfaces. To investigate these interactions, a 185-day controlled exposure experiment was conducted using Aurelia aurita polyps. Factorial combinations of microplastics (0, 0.1, 1 mg/L) and tetracycline (0, 0.5, 5 mg/L) were employed to simulate environmentally relevant pollution scenarios. Microbiome alterations were characterized using metagenomic approaches. Analysis revealed that while alpha and beta diversity measures remained unaffected at environmental concentrations, significant shifts occurred in the relative abundance of dominant bacterial taxa, including Pseudomonadota, Actinomycetota, and Mycoplasmatota. Metabolic pathway analysis demonstrated perturbations in key functional categories including cellular processes and environmental signal transduction. Furthermore, microplastic exposure was associated with modifications in polyp life-stage characteristics, suggesting potential implications for benthic-pelagic population dynamics. These findings provide evidence for the impacts of microplastic-antibiotic interactions on cnidarian holobionts, with ramifications for predicting jellyfish population responses in contaminated ecosystems.
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Affiliation(s)
- Xuandong Wu
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, Guangxi Minzu University, Nanning 530008, China; (X.W.); (H.L.)
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynethesis Chemistry, Guuangxi Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning 530007, China
| | - Hongze Liao
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, Guangxi Minzu University, Nanning 530008, China; (X.W.); (H.L.)
| | - Xiaoyong Zhang
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China;
| | - Zhenhua Ma
- Key Laboratory of Efffcient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya 572018, China;
| | - Zhilu Fu
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, Guangxi Minzu University, Nanning 530008, China; (X.W.); (H.L.)
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynethesis Chemistry, Guuangxi Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning 530007, China
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107
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Sonam W, Liu Y, Ren L. Differentiation and Interconnection of the Bacterial Community Associated with Silene nigrescens Along the Soil-To-Plant Continuum in the Sub-Nival Belt of the Qiangyong Glacier. PLANTS (BASEL, SWITZERLAND) 2025; 14:1190. [PMID: 40284077 PMCID: PMC12030249 DOI: 10.3390/plants14081190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2025] [Revised: 03/26/2025] [Accepted: 03/27/2025] [Indexed: 04/29/2025]
Abstract
Plant microbiomes provide significant fitness advantages to their plant hosts, especially in the sub-nival belt. Studies to date have primarily focused on belowground communities in this region. Here, we utilized high-throughput DNA sequencing to quantify bacterial communities in the rhizosphere soil as well as in the root and leaf endosphere compartments of Silene nigrescens to uncover the differentiation and interconnections of these bacterial communities along the soil-to-plant continuum. Our findings reveal that the bacterial communities exhibit notable variation across different plant compartment niches: the rhizosphere soil, root endosphere, and leaf endosphere. There was a progressive decline in diversity, network complexity, network modularity, and niche breadth from the rhizosphere soil to the root endosphere, and further to the leaf endosphere. Conversely, both the host plant selection effect and the stability of these communities showed an increasing trend. Total nitrogen and total potassium emerged as crucial factors accounting for the observed differences in diversity and composition, respectively. Additionally, 3.6% of the total amplicon sequence variants (ASVs) were shared across the rhizosphere soil, root endosphere, and leaf endosphere. Source-tracking analysis further revealed bacterial community migration among these compartments. The genera Pseudomonas, IMCC26256, Mycobacterium, Phyllobacterium, and Sphingomonas constituted the core of the bacterial microbiome. These taxa are shared across all three compartment niches and function as key connector species. Notably, Pseudomonas stands out as the predominant taxon among these bacteria, with nitrogen being the most significant factor influencing its relative abundance. These findings deepen our understanding of the assembly principles and ecological dynamics of the plant microbiome in the sub-nival belt, offering an integrated framework for its study.
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Affiliation(s)
- Wangchen Sonam
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongqin Liu
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Luming Ren
- Nanning Garden Expo Park Management Center, Nanning Institute of Tropical Botany, Nanning 530299, China;
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Achasova KM, Snytnikova OA, Chanushkina KE, Morozova MV, Tsentalovich YP, Kozhevnikova EN. Baseline abundance of Akkermansia muciniphila and Bacteroides acidifaciens in a healthy state predicts inflammation associated tumorigenesis in the AOM/DSS mouse model. Sci Rep 2025; 15:12241. [PMID: 40210644 PMCID: PMC11985942 DOI: 10.1038/s41598-025-96514-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2025] [Accepted: 03/28/2025] [Indexed: 04/12/2025] Open
Abstract
Numerous studies demonstrate that intestinal microbiota contribute to colorectal cancer (CRC), which is often associated with dysbiosis. Most of the data were obtained from studies on CRC patients, making it challenging to determine whether alterations in microbiota are a consequence of the pathology or whether they actively drive its progression. Several studies using laboratory animals suggest that gut microbiota may be involved in both the onset and progression of CRC. In the present study we utilized the azoxymethane-dextran sulfate sodium (AOM/DSS) mouse model of CRC to investigate the contribution of healthy-state microbiota to inflammation-associated tumorigenesis. Two cohorts of C57BL/6 mice harboring different intestinal microbiota demonstrated different susceptibility to AOM/DSS treatment. Sequencing of 16S rRNA bacterial DNA from fecal samples revealed Akkermansia muciniphila and Bacteroides acidifaciens as marker features in the healthy-state microbiota (before AOM/DSS administration), which showed a strong positive correlation with tumor incidence. Moreover, the healthy-state abundance of these markers, considered beneficial bacteria, was strongly positively correlated with the sulfate-reducing bacteria Desulfovibrio fairfieldensis identified as a marker of chronic colitis-associated microbiota. Furthermore, the abundances of these marker features, associated with CRC outcome, correlated with the expression of interferon gamma and nitric oxide synthase 2 genes in colon tissue during the early stage of DSS-induced intestinal inflammation. In contrast to multiple studies demonstrating the anti-inflammatory properties of A. muciniphila and B. acidifaciens, our results point out their potential adverse effect under specific conditions of genotoxicity and inflammation in the intestine. Taken together, our findings suggest a complex, context-dependent role of commensal microbiota in inflammation-associated dysbiosis and CRC.
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Affiliation(s)
- Kseniya M Achasova
- Scientific Research Institute of Neurosciences and Medicine, Novosibirsk, Russia, 630117
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia, 630090
| | | | | | - Maryana V Morozova
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia, 630090
| | | | - Elena N Kozhevnikova
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia, 630090.
- Laboratory of Bioengineering, Novosibirsk State Agrarian University, Novosibirsk, Russia, 630039.
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109
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Wang Z, Gao X, Ji H, Shao M, Ni B, Fei S, Sun L, Chen H, Tan R, Du M, Gu M. Characterization of gut microbiota and metabolites in renal transplant recipients during COVID-19 and prediction of one-year allograft function. J Transl Med 2025; 23:420. [PMID: 40211390 PMCID: PMC11987245 DOI: 10.1186/s12967-025-06090-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2024] [Accepted: 01/06/2025] [Indexed: 04/13/2025] Open
Abstract
BACKGROUND The gut-lung-kidney axis is pivotal in immune-related kidney diseases, with gut dysbiosis potentially exacerbating the severity of Coronavirus disease 2019 (COVID-19) in recipients of kidney transplant. This study aimed to characterize the gut microbiome and metabolome in renal transplant recipients with COVID-19 pneumonia over a one-year follow-up period. METHODS A total of 30 renal transplant recipients were enrolled, comprising 17 with COVID-19 pneumonia, six with mild COVID-19, and seven without COVID-19. Fecal samples were collected at the onset of infection for gut microbiome and metabolome analysis. Generalized Estimating Equations (GEE) model and Latent Class Growth Mixed Model (LCGMM) were employed to dissect the relationships among clinical characteristics, laboratory tests, and gut microbiota and metabolites. RESULTS Four microbial phyla (Deferribacteres, TM7, Fusobacteria, and Gemmatimonadetes) and 13 genera were significantly enriched across three recipients groups, correlating with baseline inflammatory response and allograft function. Additionally, 52 differentially expressed metabolites were identified, with seven significantly correlating with eight altered microbiota genera. LCGMM revealed two distinct classes of recipients, with those suffering from COVID-19 pneumonia exhibiting significantly elevated serum creatinine (Scr) trajectories over the one-year period. GEE further identified 12 genera and 181 metabolites closely associated with these trajectories; a multivariable model incorporating gut metabolites of 1-Caffeoylquinic Acid and PMK was found to effectively predict one-year allograft function. CONCLUSIONS Our study indicates a possible interaction between the composition of the gut microbiota and metabolites community and COVID-19 in renal transplant recipients, particularly in relation to disease severity and the prediction of one-year allograft function.
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Affiliation(s)
- Zijie Wang
- Department of Urology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003, China
| | - Xiang Gao
- Department of Urology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003, China
| | - Hongsheng Ji
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
- Departments of Environmental Genomics and Genetic Toxicology, the Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Ming Shao
- Departments of Environmental Genomics and Genetic Toxicology, the Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Bin Ni
- Department of Urology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003, China
| | - Shuang Fei
- Department of Urology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Li Sun
- Department of Urology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Hao Chen
- Department of Urology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Ruoyun Tan
- Department of Urology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China.
| | - Mulong Du
- Department of Urology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003, China.
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.
- Departments of Environmental Genomics and Genetic Toxicology, the Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.
| | - Min Gu
- Department of Urology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003, China.
- Department of Urology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China.
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Yun J, Song JS, Yoo JJ, Kweon S, Choi YY, Lim D, Kuk JC, Kim HJ, Park SK. Microbial and Immune Landscape of Malignant Ascites: Insights from Gut, Bladder, and Ascitic Fluid Analyses. Cancers (Basel) 2025; 17:1280. [PMID: 40282458 PMCID: PMC12025743 DOI: 10.3390/cancers17081280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2025] [Revised: 04/01/2025] [Accepted: 04/07/2025] [Indexed: 04/29/2025] Open
Abstract
BACKGROUND/OBJECTIVES Malignant ascites frequently arises in advanced cancers with peritoneal metastasis and is associated with poor outcomes. Known mechanisms include lymphatic obstruction by tumor cells, increased vascular permeability, and sodium retention via the renin-angiotensin-aldosterone system; however, the pathogenesis remains not fully understood. We investigated whether gut and bladder microbiomes correlate with malignant ascites development or progression and whether the immune microenvironment in ascitic fluid is altered. METHODS We enrolled 66 histologically confirmed cancer patients, dividing them into malignant ascites (n = 20) and non-ascites (n = 46) groups. Stool, urine, and ascitic fluid samples were analyzed using 16S rRNA next-generation sequencing. Immune cell subsets in ascitic fluid were characterized using flow cytometry. RESULTS In 19 of the 20 malignant ascites samples, the bacterial load was too low for reliable 16S rRNA sequencing, suggesting that malignant ascites is largely sterile. The overall gut microbiome diversity did not differ significantly by ascites status, although a trend emerged in patients with peritoneal metastasis, including the enrichment of class Clostridia and Gammaproteobacteria. Bladder microbiome analysis also showed no significant differences in ascites or metastasis status. Flow cytometry revealed reduced T-cell (CD3+, CD4+, CD8+) and NK cell (CD56+) populations compared to data from cirrhotic ascites. CONCLUSIONS Malignant ascites exhibit minimal bacterial biomass, making comprehensive microbiome analysis challenging. Although no major global changes were noted in gut and bladder microbiomes, specific taxa were linked to peritoneal metastasis. These findings highlight an immunosuppressive ascitic environment and suggest that larger-scale or multi-omics approaches may help elucidate the role of microbiota in malignant ascites.
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Affiliation(s)
- Jina Yun
- Division of Hematology-Oncology, Department of Medicine, Soonchunhyang University Bucheon Hospital, Soonchunhyang University College of Medicine, Bucheon 14584, Republic of Korea; (H.-J.K.); (S.-K.P.)
| | - Ju-Sun Song
- GC Genome, Department of Laboratory Medicine, Green Cross Laboratories, Seoul 16924, Republic of Korea; (J.-S.S.); (S.K.)
| | - Jeong-Ju Yoo
- Division of Hepatology, Department of Medicine, Soonchunhyang University Bucheon Hospital, Bucheon 14584, Republic of Korea;
| | - Solbi Kweon
- GC Genome, Department of Laboratory Medicine, Green Cross Laboratories, Seoul 16924, Republic of Korea; (J.-S.S.); (S.K.)
| | - Yoon-Young Choi
- Department of Surgery, Soonchunhyang University Bucheon Hospital, Soonchunhyang University College of Medicine, Bucheon 14584, Republic of Korea; (Y.-Y.C.); (D.L.); (J.-C.K.)
| | - Daero Lim
- Department of Surgery, Soonchunhyang University Bucheon Hospital, Soonchunhyang University College of Medicine, Bucheon 14584, Republic of Korea; (Y.-Y.C.); (D.L.); (J.-C.K.)
| | - Jung-Cheol Kuk
- Department of Surgery, Soonchunhyang University Bucheon Hospital, Soonchunhyang University College of Medicine, Bucheon 14584, Republic of Korea; (Y.-Y.C.); (D.L.); (J.-C.K.)
| | - Hyun-Jung Kim
- Division of Hematology-Oncology, Department of Medicine, Soonchunhyang University Bucheon Hospital, Soonchunhyang University College of Medicine, Bucheon 14584, Republic of Korea; (H.-J.K.); (S.-K.P.)
| | - Seong-Kyu Park
- Division of Hematology-Oncology, Department of Medicine, Soonchunhyang University Bucheon Hospital, Soonchunhyang University College of Medicine, Bucheon 14584, Republic of Korea; (H.-J.K.); (S.-K.P.)
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Cavalcante FG, Bandeira LL, Faria CMDA, Mesquita ADFN, de Matos Neto JM, Martins CM, Martins SCS. The Unseen Impacts of Human Footprints: How Land Use Reshapes Actinobacterial Communities in the Brazilian Cerrado. BIOLOGY 2025; 14:390. [PMID: 40282255 PMCID: PMC12025010 DOI: 10.3390/biology14040390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2025] [Revised: 04/04/2025] [Accepted: 04/07/2025] [Indexed: 04/29/2025]
Abstract
Evaluating microbial community changes in soils allows the understanding of ecoevolutionary dynamics, providing information on microbiome responses to anthropological interferences, reduced biodiversity, and climatic changes. The actinobacteria phylum plays crucial roles from an ecological point of view and is the focus of the present study, which tracked changes in the actinobacterial communities from Brazilian Cerrado soil in an environmental protection unit, based on different land uses. The evaluation of 16S rRNA and further taxonomical clustering of operational taxonomic units (OTUs) indicated Actinomycetales as the main order within all land uses, ranging from 45.4-70.1%, with Micrococales and Rubrobacterales being found only in agricultural soils. The evaluation of taxonomical classes revealed Actinobacteria as the main representative in all land uses (45.5-70.4%), with a paired coprevalence of Thermoleophilia (43.4%) in secondary soils, a taxon associated with phosphorus-deficient grounds. The unraveling of families and genera was most challenging due to the OTUs' dispersion given the volume of data, coupled with a high percentage of unidentified genera (71.6-86.1%), mainly in conserved and preserved areas. The reduced biodiversity, reduced undescribed taxa, and enhanced potentially pathogenic strains in anthropogenic affected sites, which suffer more from climatic changes, denote the harm that human activity causes to microbiological diversity.
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Affiliation(s)
- Fernando Gouveia Cavalcante
- National Institute of Science and Technology/Ministry of Agriculture, Livestock and Food Supply (INCT/MAPA), Aracaju 49065-310, Brazil;
- Graduate Course of Ecology and Natural Resources, Department of Biology, Federal University of Ceará, Fortaleza 60355-636, Brazil; (L.L.B.); (C.M.d.A.F.); (C.M.M.); (S.C.S.M.)
| | - Leonardo Lima Bandeira
- Graduate Course of Ecology and Natural Resources, Department of Biology, Federal University of Ceará, Fortaleza 60355-636, Brazil; (L.L.B.); (C.M.d.A.F.); (C.M.M.); (S.C.S.M.)
| | - Christiana Mara de Assis Faria
- Graduate Course of Ecology and Natural Resources, Department of Biology, Federal University of Ceará, Fortaleza 60355-636, Brazil; (L.L.B.); (C.M.d.A.F.); (C.M.M.); (S.C.S.M.)
| | | | - João Moreira de Matos Neto
- Graduate Course of Biochemistry, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza 60355-636, Brazil;
| | - Claudia Miranda Martins
- Graduate Course of Ecology and Natural Resources, Department of Biology, Federal University of Ceará, Fortaleza 60355-636, Brazil; (L.L.B.); (C.M.d.A.F.); (C.M.M.); (S.C.S.M.)
| | - Suzana Claudia Silveira Martins
- Graduate Course of Ecology and Natural Resources, Department of Biology, Federal University of Ceará, Fortaleza 60355-636, Brazil; (L.L.B.); (C.M.d.A.F.); (C.M.M.); (S.C.S.M.)
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Denny JE, Flores JN, Mdluli NV, Abt MC. Standard mouse diets lead to differences in severity in infectious and non-infectious colitis. mBio 2025; 16:e0330224. [PMID: 40126017 PMCID: PMC11980566 DOI: 10.1128/mbio.03302-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2024] [Accepted: 02/04/2025] [Indexed: 03/25/2025] Open
Abstract
Clostridioides difficile infects the large intestine and can result in debilitating and potentially fatal colitis. The intestinal microbiota is a major factor influencing the severity of disease following infection. Factors like diet that shape microbiota composition and function may modulate C. difficile colitis. Here, we report that mice fed two distinct standard mouse chows (LabDiet 5010 and LabDiet 5053) exhibited significantly different susceptibility to severe C. difficile infection. Both diets are grain-based with comparable profiles of macro and micronutrient composition. Diet 5010-fed mice had severe morbidity and mortality compared to Diet 5053-fed mice despite no differences in C. difficile colonization or toxin production. Furthermore, Diet 5053 protected mice from toxin-induced epithelial damage. This protection was microbiota-dependent as germ-free mice or mice harboring a reduced diversity microbiota fed Diet 5053 were not protected from severe infection. However, cohousing with mice harboring a complex microbiota restored the protective capacity of Diet 5053 but not Diet 5010. Metabolomic profiling revealed distinct metabolic capacities between Diet 5010- and Diet 5053-fed intestinal microbiotas. Diet 5053-mediated protection extended beyond C. difficile infection as Diet 5053-fed mice displayed less severe dextran sodium sulfate-induced colitis than Diet 5010-fed mice, highlighting a potentially broader capacity for Diet 5053 to limit colitis. These findings demonstrate that standard diet formulations in combination with the host microbiota can drive variability in severity of infectious and non-infectious murine colitis systems, and that diet holds therapeutic potential to limit the severity of C. difficile infection through modulating the functional capacity of the microbiota.IMPORTANCEDiet is a major modulator of the microbiota and intestinal health. This report finds that two different standard mouse diets starkly alter the severity of colitis observed in a pathogen-mediated (Clostridioides difficile) and non-infectious (dextran sodium sulfate) mouse colitis experimental systems. These findings in part explain study-to-study variability using these mouse systems to study disease. Since the gut microbiota plays a key role in intestinal homeostasis, diet-derived modulation of the microbiota is a promising avenue to control disease driven by intestinal inflammation and may represent a potential intervention strategy for at-risk patients.
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Affiliation(s)
- Joshua E. Denny
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Julia N. Flores
- Division of Infectious Disease, Department of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Nontokozo V. Mdluli
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Michael C. Abt
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Fagerlund A, Møretrø T, Jensen MR, Langsrud S, Moen B. Early detection and population dynamics of Listeria monocytogenes in naturally contaminated drains from a meat processing plant. Front Microbiol 2025; 16:1541481. [PMID: 40270812 PMCID: PMC12014604 DOI: 10.3389/fmicb.2025.1541481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2024] [Accepted: 03/25/2025] [Indexed: 04/25/2025] Open
Abstract
Listeria monocytogenes, a significant foodborne pathogen, often contaminates ready-to-eat foods through cross-contamination in food processing environments, and floor drains represent one of the most common sites of persistence. Subtyping of L. monocytogenes from food processing plants for the purpose of source tracking is usually performed on a single colony obtained after selective enrichment. This study investigates the temporal variation and population dynamics of L. monocytogenes in drains, focusing on the diversity of L. monocytogenes and the impact of the resident microbiota. Six different drains in a meat processing plant were each sampled four times over a period of 8 weeks and subjected to two-step selective enrichment in Half Fraser and Full Fraser broths. The clonal complexes (CCs) of at least 20 individual L. monocytogenes isolates from each positive sample (460 isolates in total) were determined using either the GenoListeria Multiplex qPCR assay or whole genome sequencing (WGS). The microbiota in drains and enrichment cultures was analyzed by 16S rRNA gene amplicon sequencing and metagenomic or quasimetagenomic sequencing. L. monocytogenes was detected in the majority of samples and four different CCs were identified - CC9, CC11 (ST451), CC121 and CC8 - with up to three CCs in the same sample and with different CCs dominating in different drains. The same clones of CC9, CC11, and CC121 had persisted in the facility for 3-5 years. The composition of the drain microbiota remained relatively stable over time, with Pseudomonas, Acinetobacter, Janthinobacterium, Chryseobacterium, Staphylococcus, and Sphingomonas as the most commonly identified genera. There were no apparent differences in the microbial genera present in L. monocytogenes positive and negative drains or samples. The study highlights the use of techniques such as qPCR and quasimetagenomics for monitoring and controlling the risk of L. monocytogenes contamination in processing environments.
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Affiliation(s)
- Annette Fagerlund
- Department of Food Safety and Quality, Nofima – Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | | | | | | | - Birgitte Moen
- Department of Food Safety and Quality, Nofima – Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
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Costa JSP, Brandão HV, da Cruz Martins C, Benevides RG, Contreras JCZ, Sparvoli LG, Vanzele PAR, Taddei CR, Vieira TDO, Vieira GO. Intestinal microbiota development in the first week of life of preterm newborns. J Pediatr (Rio J) 2025:S0021-7557(25)00055-5. [PMID: 40158530 DOI: 10.1016/j.jped.2025.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 02/21/2025] [Accepted: 02/24/2025] [Indexed: 04/02/2025] Open
Abstract
OBJECTIVE This study aimed to evaluate the intestinal microbiota development in the first week of life of preterm newborns (PTNB) treated at a public hospital in a municipality in the Brazilian Northeast. METHODS This is an observational, longitudinal, and descriptive study with 23 PTNBs. Two stool samples were collected from each neonate (fasting/meconium and seventh day of life) for stool microbiota analysis by 16S rRNA gene sequencing. The authors analyzed alpha diversity (Chao1, Shannon, and Simpson indices) and principal coordinates of beta diversity. RESULTS Forty-six stool samples from 23 PTNBs were analyzed at the taxonomic level. Microbiota's development was dynamic with low diversity. The authors observed a statistical association with the genera Enterobacterales, Streptococcus, Bacteroides, Clostridium_sensu_stricto_1, Enterococcus, and Bifidobacterium in the fasting samples when compared to the day-7 samples. The genus Staphylococcus also dominated at both times. CONCLUSION Dynamics were observed in the intestinal microbiota development, with an alpha diversity decrease in the stool samples collected at fasting/meconium and on the seventh day of life.
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Affiliation(s)
| | - Heli Vieira Brandão
- Universidade Estadual de Feira de Santana (UEFS), Feira de Santana, BA, Brazil
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115
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Arenas-Montes J, Alcala-Diaz JF, Garcia-Fernandez H, Gutierrez-Mariscal FM, Lopez-Moreno A, Luque-Cordoba D, Arenas-de Larriva AP, Torres-Peña JD, Luque RM, Prodam F, Priego-Capote F, Delgado-Lista J, Lopez-Miranda J, Camargo A. A microbiota pattern associated with cardiovascular events in secondary prevention: the CORDIOPREV study. Eur Heart J 2025:ehaf181. [PMID: 40197788 DOI: 10.1093/eurheartj/ehaf181] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 08/21/2024] [Accepted: 03/11/2025] [Indexed: 04/10/2025] Open
Abstract
BACKGROUND AND AIMS Preventing new cardiovascular events in patients with established cardiovascular disease (CVD) is a daunting task for clinicians. Intestinal microbiota may help identify patients at risk, thus improving the strategies of secondary prevention. The aim of this study was to evaluate the baseline differences between the gut microbiota from coronary heart disease (CHD) patients suffering new major adverse cardiovascular events (MACEs) in the following 7 years, compared with CHD patients who did not undergo new MACE in this period, and to build a score associated with the risk of suffering new MACE. METHODS Within the framework of the CORDIOPREV study, a clinical trial that involved 1002 patients with CHD, intestinal microbiota was examined in patients with available faecal samples (n = 679, 132 MACE), through 16S metagenomics on the Illumina MiSeq and Quiime2 software. Lipopolysaccharide (LPS) was measured using limulus amoebocyte lysate test. RESULTS Random survival forest identified 10 bacterial taxa with a higher predictive power for MACE incidence. Receiver operating characteristic curves yielded an area under the curve of 65.2% (59.1%-71.3%) in the training set and 68.6% (59.3%-77.9%) in the validation set. The intestinal microbiota risk score was associated with a MACE incidence hazard ratio of 2.01 (95% confidence interval 1.37-3.22). Lipopolysaccharide analysis showed a greater LPS post-prandial fold change in the MACE group (P = .005). CONCLUSIONS These results reinforce the relationship between intestinal microbiota and CVD and suggest that a microbiota profile is associated with MACE in CHD patients, in addition to higher endotoxaemia.
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Affiliation(s)
- Javier Arenas-Montes
- Lipids and Atherosclerosis Unit, Department of Internal Medicine, Hospital Universitario Reina Sofía, Cordoba 14004, Spain
- Department of Medical and Surgical Sciences, Universidad de Cordoba, Cordoba 14004, Spain
- Maimonides Institute for Biomedical Research in Cordoba (IMIBIC), Cordoba 14004, Spain
- CIBER Fisiopatologia Obesidad y Nutricion (CIBEROBN), Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Juan F Alcala-Diaz
- Lipids and Atherosclerosis Unit, Department of Internal Medicine, Hospital Universitario Reina Sofía, Cordoba 14004, Spain
- Department of Medical and Surgical Sciences, Universidad de Cordoba, Cordoba 14004, Spain
- Maimonides Institute for Biomedical Research in Cordoba (IMIBIC), Cordoba 14004, Spain
- CIBER Fisiopatologia Obesidad y Nutricion (CIBEROBN), Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Helena Garcia-Fernandez
- Lipids and Atherosclerosis Unit, Department of Internal Medicine, Hospital Universitario Reina Sofía, Cordoba 14004, Spain
- Department of Medical and Surgical Sciences, Universidad de Cordoba, Cordoba 14004, Spain
- Maimonides Institute for Biomedical Research in Cordoba (IMIBIC), Cordoba 14004, Spain
- CIBER Fisiopatologia Obesidad y Nutricion (CIBEROBN), Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Francisco M Gutierrez-Mariscal
- Lipids and Atherosclerosis Unit, Department of Internal Medicine, Hospital Universitario Reina Sofía, Cordoba 14004, Spain
- Department of Medical and Surgical Sciences, Universidad de Cordoba, Cordoba 14004, Spain
- Maimonides Institute for Biomedical Research in Cordoba (IMIBIC), Cordoba 14004, Spain
- CIBER Fisiopatologia Obesidad y Nutricion (CIBEROBN), Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Alejandro Lopez-Moreno
- Lipids and Atherosclerosis Unit, Department of Internal Medicine, Hospital Universitario Reina Sofía, Cordoba 14004, Spain
- Department of Medical and Surgical Sciences, Universidad de Cordoba, Cordoba 14004, Spain
- Maimonides Institute for Biomedical Research in Cordoba (IMIBIC), Cordoba 14004, Spain
- CIBER Fisiopatologia Obesidad y Nutricion (CIBEROBN), Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Diego Luque-Cordoba
- Maimonides Institute for Biomedical Research in Cordoba (IMIBIC), Cordoba 14004, Spain
- Department of Analytical Chemistry, Annex Marie Curie Building, Campus of Rabanales, University of Cordoba, Cordoba 14071, Spain
- Consortium for Biomedical Research in Frailty & Healthy Ageing, CIBERFES, Carlos III Institute of Health, Madrid 28029, Spain
| | - Antonio P Arenas-de Larriva
- Lipids and Atherosclerosis Unit, Department of Internal Medicine, Hospital Universitario Reina Sofía, Cordoba 14004, Spain
- Department of Medical and Surgical Sciences, Universidad de Cordoba, Cordoba 14004, Spain
- Maimonides Institute for Biomedical Research in Cordoba (IMIBIC), Cordoba 14004, Spain
- CIBER Fisiopatologia Obesidad y Nutricion (CIBEROBN), Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Jose D Torres-Peña
- Lipids and Atherosclerosis Unit, Department of Internal Medicine, Hospital Universitario Reina Sofía, Cordoba 14004, Spain
- Department of Medical and Surgical Sciences, Universidad de Cordoba, Cordoba 14004, Spain
- Maimonides Institute for Biomedical Research in Cordoba (IMIBIC), Cordoba 14004, Spain
- CIBER Fisiopatologia Obesidad y Nutricion (CIBEROBN), Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Raul M Luque
- Maimonides Institute for Biomedical Research in Cordoba (IMIBIC), Cordoba 14004, Spain
- CIBER Fisiopatologia Obesidad y Nutricion (CIBEROBN), Instituto de Salud Carlos III, Madrid 28029, Spain
- Department of Cell Biology, Physiology and Immunology, University of Cordoba, Cordoba 14071, Spain
| | - Flavia Prodam
- Department of Health Sciences, Unit of Endocrinology, Università del Piemonte Orientale, Novara 28100, Italy
| | - Feliciano Priego-Capote
- Maimonides Institute for Biomedical Research in Cordoba (IMIBIC), Cordoba 14004, Spain
- Department of Analytical Chemistry, Annex Marie Curie Building, Campus of Rabanales, University of Cordoba, Cordoba 14071, Spain
- Consortium for Biomedical Research in Frailty & Healthy Ageing, CIBERFES, Carlos III Institute of Health, Madrid 28029, Spain
| | - Javier Delgado-Lista
- Lipids and Atherosclerosis Unit, Department of Internal Medicine, Hospital Universitario Reina Sofía, Cordoba 14004, Spain
- Department of Medical and Surgical Sciences, Universidad de Cordoba, Cordoba 14004, Spain
- Maimonides Institute for Biomedical Research in Cordoba (IMIBIC), Cordoba 14004, Spain
- CIBER Fisiopatologia Obesidad y Nutricion (CIBEROBN), Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Jose Lopez-Miranda
- Lipids and Atherosclerosis Unit, Department of Internal Medicine, Hospital Universitario Reina Sofía, Cordoba 14004, Spain
- Department of Medical and Surgical Sciences, Universidad de Cordoba, Cordoba 14004, Spain
- Maimonides Institute for Biomedical Research in Cordoba (IMIBIC), Cordoba 14004, Spain
- CIBER Fisiopatologia Obesidad y Nutricion (CIBEROBN), Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Antonio Camargo
- Lipids and Atherosclerosis Unit, Department of Internal Medicine, Hospital Universitario Reina Sofía, Cordoba 14004, Spain
- Department of Medical and Surgical Sciences, Universidad de Cordoba, Cordoba 14004, Spain
- Maimonides Institute for Biomedical Research in Cordoba (IMIBIC), Cordoba 14004, Spain
- CIBER Fisiopatologia Obesidad y Nutricion (CIBEROBN), Instituto de Salud Carlos III, Madrid 28029, Spain
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Lázaro Á, Gómez-Ramírez P, Vila-Donat P, Cimbalo A, Manyes L. Effects of pumpkin and fermented whey on fecal microbiota profile against AFB1 and OTA exposure in Wistar rats. Toxicol Mech Methods 2025:1-13. [PMID: 40129370 DOI: 10.1080/15376516.2025.2484636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2025] [Revised: 03/20/2025] [Accepted: 03/21/2025] [Indexed: 03/26/2025]
Abstract
Mycotoxins perturb the gut microbiota performance. Bioactive compounds have been recently used as a new food strategy to diminish mycotoxins bioaccessibility and prevent their toxic effects on human and animal health. Male and female Wistar rats were exposed orally to twelve different diets containing aflatoxin B1 (AFB1) and/or ochratoxin A (OTA) with or without fermented whey (FW) and pumpkin (P) for 28 days. Fecal microbiota using 16S rRNA gene sequencing and subsequent metagenomics analysis were analyzed to study the effect of 28-day exposure through diet of contaminated and enriched feed. QIIME 2 microbiome analysis package (version 2024.5) was used to analyze the demultiplexed data. Mycotoxins-functional ingredients combination contributed more to microbial phylogenetic faith α-diversity rather than the functional ingredients alone, while the same combination reported a microbial α-diversity enhancement in comparison to the mycotoxins alone. Proteobacteria phylum was reduced in rat samples fed with contaminated diets (AFB1, OTA, and AFB1+OTA), while there was an increase-although not in all groups-when adding the functional ingredients. The main difference between the sexes was found in FW+AFB1+OTA group, with males (25%) showing higher % of Proteobacteria than females (1.86%). Phylogenetic diversity faith only focuses on microbial genetic (dis)similarity, not considering the biological function. Morganella morganii, a Proteobacteria found in some groups presents anticancer activity, but it is also related to inflammatory bowel disease and colorectal cancer. To sum up, both mycotoxins and functional ingredients trigger changes in the microbiota profile of Wistar rats in a sex-specific manner.
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Affiliation(s)
- Álvaro Lázaro
- Biotech Agrifood, University of Valencia, Burjassot, Spain
| | - Pilar Gómez-Ramírez
- Area of Toxicology, Department of Health Sciences, University of Murcia, Murcia, Spain
| | | | | | - Lara Manyes
- Biotech Agrifood, University of Valencia, Burjassot, Spain
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De La Guardia Hidrogo VM, Rummell LM, Swanson KS. Effects of Yeast Products on the Apparent Total Tract Macronutrient Digestibility, Oxidative Stress Markers, Skin Measures, and Fecal Characteristics and Microbiota Populations of Healthy Adult Dogs. Animals (Basel) 2025; 15:1046. [PMID: 40218439 PMCID: PMC11987801 DOI: 10.3390/ani15071046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2025] [Revised: 04/01/2025] [Accepted: 04/01/2025] [Indexed: 04/14/2025] Open
Abstract
Brewer's yeast has high nutritional value and contains bioactive compounds that may promote health. Functionalized canola meal (FCM) is a high-fiber ingredient that has been proposed as a carrier for brewer's yeast. The objective of this experiment was to determine the apparent total tract digestibility (ATTD) of diets containing yeast-enriched FCM and test their effects on the fecal characteristics and microbiota, skin measures, and serum oxidative stress markers of adult dogs. Twelve dogs were fed four extruded kibble diets (control (no FCM or yeast), FCM + low yeast dose, FCM + medium yeast dose, and FCM + high yeast dose) in a replicated 4x4 LSD. Dogs fed yeast-enriched FCM had greater wet fecal output (~15% greater than control). The ATTD of DM, OM, and fat was lower in the diets containing FCM, although the values remained >80% for all macronutrients. The yeast-enriched FCM altered the relative abundance of a few bacterial genera (Eubacterium brachy, Peptoclostridium, Ruminococcus gnavus) and fecal phenol and indole concentrations. Other fecal characteristics, metabolites, bacterial diversity indices, skin measures, or oxidative stress markers were not affected. These findings suggest that yeast-enriched FCM can be incorporated into canine diets without compromising stool quality or nutrient digestibility and may affect microbial metabolism.
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Affiliation(s)
| | | | - Kelly S. Swanson
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Department of Veterinary Clinical Medicine, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
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Plaza-Díaz J, Fernández MF, García F, Chueca N, Fontana L, Álvarez-Mercado AI. Comparison of Three DNA Isolation Methods and Two Sequencing Techniques for the Study of the Human Microbiota. Life (Basel) 2025; 15:599. [PMID: 40283154 PMCID: PMC12028492 DOI: 10.3390/life15040599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2025] [Revised: 03/21/2025] [Accepted: 04/02/2025] [Indexed: 04/07/2025] Open
Abstract
Breast cancer is the most commonly diagnosed cancer in women and the second leading cause of female death. Altered interactions between the host and the gut microbiota appear to play an influential role in carcinogenesis. Several studies have shown different signatures of the gut microbiota in patients with breast cancer compared to healthy women. Currently, there is disagreement regarding the different DNA isolation and sequencing methodologies for studies on the human microbiota, given that they can influence the interpretation of the results obtained. The goal of this work was to compare (1) three different DNA extraction strategies to minimize the impact of human DNA, and (2) two sequencing strategies (16S rRNA and shotgun) to identify discrepancies in microbiome results. We made use of breast tissue and fecal samples from both healthy women and breast cancer patients who participated in the MICROMA study (reference NCT03885648). DNA was isolated by means of mechanical lysis, trypsin, or saponin. The amount of eukaryotic DNA isolated using the trypsin and saponin methods was lower compared to the mechanical lysis method (mechanical lysis, 89.11 ± 2.32%; trypsin method, 82.63 ± 1.23%; saponin method, 80.53 ± 4.09%). In samples with a predominance of prokaryotic cells, such as feces, 16S rRNA sequencing was the most advantageous approach. For other tissues, which are expected to have a more complex microbial composition, the need for an in-depth evaluation of the multifactorial interaction between the various components of the microbiota makes shotgun sequencing the most appropriate method. As for the three extraction methods evaluated, when sequencing samples other than stool, the trypsin method is the most convenient. For fecal samples, where contamination by host DNA is low, no prior treatment is necessary.
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Affiliation(s)
- Julio Plaza-Díaz
- Institute of Biosanitary Research (ibs.GRANADA), San Cecilio University Clinical Hospital, 18012 Granada, Spain; (J.P.-D.); (M.F.F.); (F.G.); (N.C.)
- School of Health Sciences, International University of La Rioja, 26001 Logroño, Spain
| | - Mariana F. Fernández
- Institute of Biosanitary Research (ibs.GRANADA), San Cecilio University Clinical Hospital, 18012 Granada, Spain; (J.P.-D.); (M.F.F.); (F.G.); (N.C.)
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
- Department of Radiology and Physical Medicine, School of Medicine, University of Granada, 18016 Granada, Spain
| | - Federico García
- Institute of Biosanitary Research (ibs.GRANADA), San Cecilio University Clinical Hospital, 18012 Granada, Spain; (J.P.-D.); (M.F.F.); (F.G.); (N.C.)
- Microbiology Unit, San Cecilio University Clinical Hospital, 18016 Granada, Spain
- Spanish Consortium for Research on Infectious Diseases (CIBERINFEC), 28029 Madrid, Spain
| | - Natalia Chueca
- Institute of Biosanitary Research (ibs.GRANADA), San Cecilio University Clinical Hospital, 18012 Granada, Spain; (J.P.-D.); (M.F.F.); (F.G.); (N.C.)
- Microbiology Unit, San Cecilio University Clinical Hospital, 18016 Granada, Spain
- Spanish Consortium for Research on Infectious Diseases (CIBERINFEC), 28029 Madrid, Spain
| | - Luis Fontana
- Institute of Biosanitary Research (ibs.GRANADA), San Cecilio University Clinical Hospital, 18012 Granada, Spain; (J.P.-D.); (M.F.F.); (F.G.); (N.C.)
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071 Granada, Spain
- Institute of Nutrition and Food Technology “José Matáix”, Centre of Biomedical Research, University of Granada, 18016 Granada, Spain
| | - Ana I. Álvarez-Mercado
- Institute of Biosanitary Research (ibs.GRANADA), San Cecilio University Clinical Hospital, 18012 Granada, Spain; (J.P.-D.); (M.F.F.); (F.G.); (N.C.)
- Institute of Nutrition and Food Technology “José Matáix”, Centre of Biomedical Research, University of Granada, 18016 Granada, Spain
- Department Pharmacology, School of Pharmacy, 18071 Granada, Spain
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Zilberstein NF, Engen PA, Swanson GR, Naqib A, Post Z, Alutto J, Green SJ, Shaikh M, Lawrence K, Adnan D, Zhang L, Voigt RM, Schwartz J, Keshavarzian A. The Bidirectional Effects of Periodontal Disease and Oral Dysbiosis on Gut Inflammation in Inflammatory Bowel Disease. J Crohns Colitis 2025; 19:jjae162. [PMID: 39447062 PMCID: PMC12041420 DOI: 10.1093/ecco-jcc/jjae162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Indexed: 10/26/2024]
Abstract
BACKGROUND AND AIMS Inflammatory bowel disease (IBD) flares can lead to excessive morbidity and mortality. This study aimed to determine whether oral dysbiosis/periodontal disease (PD) is common in IBD and is associated with disease activity in IBD. METHODS This single-center, prospective, cross-sectional, proof-of-concept, and observational study assessed the frequency of periodontal inflammatory disease and interrogated oral and stool microbiota using 16S rRNA gene amplicon sequencing of active-IBD (aIBD), inactive-IBD (iIBD), and healthy controls (HC). Questionnaires assessed diet, alcohol usage, oral hygiene behavior, and disease activity. A subset of participants underwent comprehensive dental examinations to evaluate PD. RESULTS Periodontal disease was severer in aIBD subjects than in HC, as aIBD had poorer quality diets (lower Mediterranean diet scores) than iIBD and HC. Significant differences in microbial community structure were observed in unstimulated saliva, stimulated saliva, gingiva, and stool samples, primarily between aIBD and HC. Saliva from aIBD had higher relative abundances of putative oral pathobionts from the genera Streptococcus, Granulicatella, Rothia, and Actinomyces relative to HC, despite similar oral hygiene behaviors between groups. CONCLUSIONS Our study suggests that patients with aIBD have severer periodontal disorders and higher relative abundances of putative 'pro-inflammatory' microbiota in their oral cavity, despite normal oral hygiene behaviors. Our data are consistent with the potential presence of an oral-gut inflammatory axis that could trigger IBD flare-ups in at-risk patients. Routine dental health assessments in all IBD patients should be encouraged as part of the health maintenance of IBD and as a potential strategy to decrease the risk of IBD flares.
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Affiliation(s)
- Netanel F Zilberstein
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, USA
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Rush Medical College, Chicago, IL, USA
| | - Phillip A Engen
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Rush Medical College, Chicago, IL, USA
| | - Garth R Swanson
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, USA
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Rush Medical College, Chicago, IL, USA
- Department of Anatomy and Cell Biology, Rush University Medical Center, Chicago, IL, USA
| | - Ankur Naqib
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Rush Medical College, Chicago, IL, USA
- Genomics and Microbiome Core Facility, Rush University Medical Center, Rush Medical College, Chicago, IL, USA
| | - Zoe Post
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, USA
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Rush Medical College, Chicago, IL, USA
| | - Julian Alutto
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Stefan J Green
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, USA
- Genomics and Microbiome Core Facility, Rush University Medical Center, Rush Medical College, Chicago, IL, USA
| | - Maliha Shaikh
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Rush Medical College, Chicago, IL, USA
| | - Kristi Lawrence
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Rush Medical College, Chicago, IL, USA
| | - Darbaz Adnan
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Rush Medical College, Chicago, IL, USA
| | - Lijuan Zhang
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, USA
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Rush Medical College, Chicago, IL, USA
| | - Robin M Voigt
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, USA
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Rush Medical College, Chicago, IL, USA
- Department of Anatomy and Cell Biology, Rush University Medical Center, Chicago, IL, USA
| | - Joel Schwartz
- Department of Oral Medicine and Diagnostic Sciences, University of Illinois Chicago, Chicago, IL, USA
| | - Ali Keshavarzian
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, USA
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Rush Medical College, Chicago, IL, USA
- Department of Anatomy and Cell Biology, Rush University Medical Center, Chicago, IL, USA
- Department of Physiology, Rush University Medical Center, Chicago, IL, USA
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Adam-Beyer N, Deusner C, Schmidt M, Perner M. Microbial hydrogen oxidation potential in seasonally hypoxic Baltic Sea sediments. Front Microbiol 2025; 16:1565157. [PMID: 40256623 PMCID: PMC12007115 DOI: 10.3389/fmicb.2025.1565157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2025] [Accepted: 03/20/2025] [Indexed: 04/22/2025] Open
Abstract
The majority of the organic matter (OM) degradation on the seafloor occurs in coastal regions. Since oxygen (O2) becomes quickly depleted in the top sediments, most of the OM decomposition is driven by microbial sulfate reduction (SR) and fermentation, the latter generating molecular hydrogen (H2). If the H2 is not consumed by hydrogenotrophic microorganisms and accumulates in the sedimentary porewaters, OM degradation is hindered. Despite the importance of H2 scavenging microorganisms for OM mineralization, the knowledge on H2 oxidizers and their constraints in coastal marine sediments is still quite limited. Here we investigated the role of H2 oxidizers in top (2 to 5 cm, suboxic-sulfidic) and bottom (18 to 22 cm, sulfidic) coastal sediments from a location exposed to seasonal hypoxia in the SW Baltic Sea. We used sediments from April, May and August, representative of different seasons. We spiked respective sediment slurries with H2 and incubated them for up to 4 weeks under O2-free conditions. H2 consumption potential, methane production and shifts in bacterial and archaeal 16S rRNA gene amplicons (generated from RNA) were assessed over time. The seasonal variations in sedimentary community compositions and pore water geochemistry already gave distinct starting conditions for the H2 enrichments. Sediments exposed to near anoxic bottom water conditions favored a microbial starter community exhibiting the highest H2 oxidation potential. Most of the observed H2 oxidation potential appeared associated with hydrogenotrophic sulfate reducers. The putative involvement of massively enriched ANME in H2 cycling in May 18 to 22 cm sediment horizons is conspicuous. While the differences in the observed H2 oxidation potentials in the studied sediment slurries are likely related to the (season-depending) overall redox state of the sediments and interstitial waters, the influence of microbial interconnections could not be fully resolved and evaluated, demonstrating the need for further consumption- and community-based studies.
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Affiliation(s)
- Nicole Adam-Beyer
- Geomicrobiology, Marine Geosystems, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Christian Deusner
- Benthic Biogeochemistry, Marine Geosystems, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Mark Schmidt
- Benthic Biogeochemistry, Marine Geosystems, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Mirjam Perner
- Geomicrobiology, Marine Geosystems, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
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Olson EG, Dittoe DK, Chaney WE, Binnebose AM, Ricke SC. Potential of saccharomyces cerevisiae fermentation-derived postbiotic technology in mitigating multiple drug-resistant Salmonella enterica serovars in an in vitro broiler cecal model. PLoS One 2025; 20:e0320977. [PMID: 40179087 PMCID: PMC11967930 DOI: 10.1371/journal.pone.0320977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2024] [Accepted: 02/27/2025] [Indexed: 04/05/2025] Open
Abstract
Diamond V Original XPC® is a Saccharomyces cerevisiae fermentation-derived postbiotic technology (SCFP) designed to interact synergistically with the animal to provide health benefits by enhancing immune function, supporting digestive integrity and absorption, and maintaining gastrointestinal (GIT) microbial balance in the host. The current study investigated the effects of 1.25% SCFP on multidrug-resistant (MDR) Salmonella serovars: S. Typhimurium (ATCC 14028), S. Enteritidis, S. Infantis, S. Heidelberg, S. Typhimurium DT104, and S. Reading, and shifts in cecal microbiota populations. Using an anaerobic in vitro poultry cecal model, cecal contents were inoculated with ~ 108 colony forming units (CFU) of MDR Salmonella serovars and incubated for 24 h at 37°C anaerobically. The treatments included: control group consisting of 0.2 g of crushed poultry feed, and a treatment group 0.25 g of feed + 1.25% inclusion of Original XPC® (SCFP). The SCFP significantly reduced five of the six serovars: S. Typhimurium ATCC, S. Enteritidis, S. Infantis, S. Heidelberg, and S. Reading (P < 0.05). Time significantly impacted S. Typhimurium DT104 reduction (P < 0.001). The most significant decrease was observed for S. Enteritidis (3.9 log10 CFU/mL), followed by S. Heidelberg (3.8 log10 CFU/mL), S. Infantis (3.4 log10 CFU/mL), S. Typhimurium ATCC (3 log10 CFU/mL), and S. Reading (1.8 log10 CFU/mL) compared to controls that averaged approximately 1 log10 CFU/mL reduction. Microbiota analysis at 24 h involved genomic DNA extraction, amplification using custom dual-indexed primers, and sequencing on the Illumina MiSeq platform. Sequencing data were analyzed using QIIME2-2021.11. S. Infantis and S. Heidelberg inoculated samples were the only groups that significantly enhanced microbial richness and evenness with SCFP addition at 24 h (P < 0.05). Pairwise comparisons revealed that samples inoculated with S. Reading and S. Typhimurium DT104 exhibited a minor change in microbial composition with SCFP, compared to other serovars that demonstrated increased microbial diversity with SCFP. Additionally, S. Infantis and S. Heidelberg inoculated samples exhibited phylogenetic diversity and microbial abundance with SCFP compared to controls at 24 h (P < 0.05). Lachnospiraceae CHKCI001 was significantly more abundant in SCFP-treated samples compared to controls (ANCOM, P < 0.05), suggesting SCFP impact on cecal fermenters and production of fermentation end products that may impact the ecosystem and inhibit pathogen growth. Although various serovars may exhibit somewhat different responses, SCFP effectively mitigated multiple MDR serovars of Salmonella under in vitro incubation conditions.
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Affiliation(s)
- Elena G. Olson
- Animal and Dairy Sciences Department, Meat Science and Animal Biologics Discovery Program, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Dana K. Dittoe
- Department of Animal Science, University of Wyoming, Laramie, Wyoming, United States of America
| | - W. Evan Chaney
- Cargill, Inc., Micronutrition and Health Solutions, Wayzata, Minnesota, United States of America
| | - Andrea M. Binnebose
- Cargill, Inc., Micronutrition and Health Solutions, Wayzata, Minnesota, United States of America
| | - Steven C. Ricke
- Animal and Dairy Sciences Department, Meat Science and Animal Biologics Discovery Program, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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Schenkelaars N, Wekema L, Faas MM, Steegers-Theunissen RP, Schoenmakers S. Protocol of the PROMOTE study: characterization of the microbiome, the immune response, and one-carbon metabolism in preconceptional and pregnant women with and without obesity (an observational subcohort of the Rotterdam Periconception cohort). PLoS One 2025; 20:e0319618. [PMID: 40173397 PMCID: PMC11964453 DOI: 10.1371/journal.pone.0319618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2024] [Accepted: 02/04/2025] [Indexed: 04/04/2025] Open
Abstract
INTRODUCTION Preconceptional and maternal obesity are well-known risk factors for pregnancy and fetal complications including gestational diabetes, hypertensive disorders, and macrosomia. Maternal obesity is associated with offspring obesity and increased healthcare costs. To disrupt the cycle of obesity, we aim to investigate the impact of the composition of the maternal microbiota (bacteria and viruses) throughout preconception and pregnancy and the associations with the immune responses and one-carbon metabolism (1-CM) as an underlying mechanism in the pathophysiology of increased adverse pregnancy outcomes in maternal obesity. METHODS AND ANALYSIS The PROMOTE study is a subcohort of the Rotterdam Periconceptional Cohort, a hospital-based observational cohort study. We will include 70 women per BMI group: ≥ 30 kg/m2 or 18.5-25 kg/m2, at different time points in each group: 10 preconceptional, 50 in the first trimester (with longitudinal follow-up during pregnancy, delivery and postpartum) and 10 in the third trimester of pregnancy. Which makes a total of 140 inclusions. Vaginal and rectal bacteriome, virome, and blood samples are collected. In the third trimester inclusions, only faecal samples are collected. Microbiota samples will be analysed using 16S rRNA sequencing. Bacteriome and virome profiles are compared between the BMI subgroups, associations with general immune responses and 1-CM markers will be shown. TRIAL REGISTRATION ClinicalTrials.gov (NCT05754645).
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Affiliation(s)
- Nicole Schenkelaars
- Department of Obstetrics and Gynaecology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Lieske Wekema
- Department of Pathology and Medical Biology, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
| | - Marijke M. Faas
- Department of Pathology and Medical Biology, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
| | | | - Sam Schoenmakers
- Department of Obstetrics and Gynaecology, Erasmus Medical Center, Rotterdam, The Netherlands
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Jonjić A, Dolanc I, Slivšek G, Bočkor L, Tarle M, Mustapić S, Kmet M, Orehovec B, Kučan Brlić P, Cokarić Brdovčak M, Obad A, Walenta M, Dražić I, Bilić-Zulle L, Lukšić I, Bulić N, Goessler W, Jonjić S, Čoklo M, Žučko J. Relationship Between Gut Microbiota and the Clinical Course of COVID-19 Disease. Viruses 2025; 17:520. [PMID: 40284963 PMCID: PMC12031135 DOI: 10.3390/v17040520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2024] [Revised: 03/26/2025] [Accepted: 03/27/2025] [Indexed: 04/29/2025] Open
Abstract
Possible early detection of people at increased risk for severe COVID-19 clinical course is extremely important so that appropriate therapy can be initiated promptly to prevent numerous deaths. Our study included 45 patients treated for COVID-19 at Dubrava University Hospital, with clinical course analysed from medical records and stool samples collected for determination of the gut microbiota diversity using 16S rRNA analysis. Sequencing was successful for 41 samples belonging to four clinical course groups (WHO guidelines): 12 samples-critical, 12-severe, 9-moderate and 8-mild group. Microbial composition was assessed between groups using two approaches-ANCOM (QIIME2) and Kruskal-Wallis (MicrobiomeAnalyst). On the genus level, two taxa were found to be differentially abundant: archaeal Halococcus and Coprococcus (for both W = 37)-the two were most abundant in the critical group (10% and 0.94% of entire abundance, respectively). Coprococcus catus was the only species identified by both methods to be differentially abundant between groups and was most abundant in the critical group. Alpha diversity indicated greater evenness of features in the critical group. Beta diversity showed clustering of samples from the critical group. A relationship between gut microbiota composition and the clinical course of COVID-19 disease was indicated, pointing towards specific distinct features of the critical group. In a broader sense, our findings might be useful in combating potential future similar pandemics and emerging virus outbreaks.
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Affiliation(s)
- Antonija Jonjić
- Institute for Anthropological Research, 10000 Zagreb, Croatia; (I.D.); (G.S.); (L.B.)
| | - Ivan Dolanc
- Institute for Anthropological Research, 10000 Zagreb, Croatia; (I.D.); (G.S.); (L.B.)
| | - Goran Slivšek
- Institute for Anthropological Research, 10000 Zagreb, Croatia; (I.D.); (G.S.); (L.B.)
| | - Luka Bočkor
- Institute for Anthropological Research, 10000 Zagreb, Croatia; (I.D.); (G.S.); (L.B.)
| | - Marko Tarle
- Dubrava University Hospital, 10000 Zagreb, Croatia; (M.T.); (M.K.); (B.O.); (I.L.)
- School of Dental Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Sanda Mustapić
- Dubrava University Hospital, 10000 Zagreb, Croatia; (M.T.); (M.K.); (B.O.); (I.L.)
| | - Marta Kmet
- Dubrava University Hospital, 10000 Zagreb, Croatia; (M.T.); (M.K.); (B.O.); (I.L.)
| | - Biserka Orehovec
- Dubrava University Hospital, 10000 Zagreb, Croatia; (M.T.); (M.K.); (B.O.); (I.L.)
| | - Paola Kučan Brlić
- Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (P.K.B.); (M.C.B.); (L.B.-Z.); (S.J.)
| | - Maja Cokarić Brdovčak
- Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (P.K.B.); (M.C.B.); (L.B.-Z.); (S.J.)
| | - Ante Obad
- University Department of Health Studies, University of Split, 21000 Split, Croatia;
| | - Martin Walenta
- Institute of Chemistry, Analytical Chemistry, University of Graz, 8010 Graz, Austria; (M.W.); (W.G.)
| | - Ivan Dražić
- Faculty of Engineering, University of Rijeka, Vukovarska 58, 51000 Rijeka, Croatia; (I.D.); (N.B.)
| | - Lidija Bilić-Zulle
- Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (P.K.B.); (M.C.B.); (L.B.-Z.); (S.J.)
- Rijeka University Hospital Centre, 51000 Rijeka, Croatia
| | - Ivica Lukšić
- Dubrava University Hospital, 10000 Zagreb, Croatia; (M.T.); (M.K.); (B.O.); (I.L.)
- School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Neven Bulić
- Faculty of Engineering, University of Rijeka, Vukovarska 58, 51000 Rijeka, Croatia; (I.D.); (N.B.)
| | - Walter Goessler
- Institute of Chemistry, Analytical Chemistry, University of Graz, 8010 Graz, Austria; (M.W.); (W.G.)
| | - Stipan Jonjić
- Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; (P.K.B.); (M.C.B.); (L.B.-Z.); (S.J.)
| | - Miran Čoklo
- Institute for Anthropological Research, 10000 Zagreb, Croatia; (I.D.); (G.S.); (L.B.)
| | - Jurica Žučko
- Faculty of Food Technology and Biotechnology, University of Zagreb, 10000 Zagreb, Croatia;
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Deng Z, Yang W, Lin T, Wang Y, Hua X, Jiang X, Chen J, Liu D, Ye Z, Zhang Y, Lynch M, Long H, Pan J. Multidimensional insights into the biodiversity of Streptomyces in soils of China: a pilot study. Microbiol Spectr 2025; 13:e0169224. [PMID: 40172189 PMCID: PMC12054067 DOI: 10.1128/spectrum.01692-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Accepted: 02/11/2025] [Indexed: 04/04/2025] Open
Abstract
Streptomyces, a diverse group of filamentous bacteria found predominantly in soil, play a crucial role in nutrient cycling and produce many valuable secondary metabolites for the pharmaceutical industry. In this pilot study, we collected 19 soil samples from 14 provinces in China to preliminarily investigate the biodiversity and genetic structure of Streptomyces in soils of China from different dimensions, using recently developed cost-efficient amplicon and whole-genome library preparation methods. Amplicon analysis showed that Actinobacteria were among the most abundant bacteria, with 0.3% of amplicon sequence variants (ASVs) belonging to Streptomyces. Meanwhile, we successfully isolated 136 Streptomyces natural strains and assembled their genomes, including 26 previously unreported species, underscoring the need for further exploration of soil Streptomyces in China. Population genetics analysis revealed that homologous recombination may primarily drive the extensive genetic diversity observed in Streptomyces, as well as a complex population structure. Complementing this, pan-genome analysis shed light on gene diversity within Streptomyces and led to the discovery of rare genes, further emphasizing the vast genetic diversity of this genus. Additionally, multiple metabolic gene clusters were found in these Streptomyces strains, as well as some potentially unique or uncommon ones were found. These findings not only highlight the biological and metabolic diversity of Streptomyces but also provide a technical framework for future studies on the global biodiversity and evolution of this genus. IMPORTANCE Streptomyces, a prominent group of Actinobacteria, holds significant importance in ecosystems and biotechnology due to their diverse array of metabolic products. However, research on the biodiversity of soil Streptomyces across extensive geographical scales in China has been limited, and their genetic diversity has rarely been evaluated using modern population genetics principles. This pilot study successfully addresses these gaps by conducting a preliminary exploration on the biodiversity of Streptomyces in Chinese soils from multiple perspectives, providing valuable insights for a deeper understanding of their biodiversity and a novel technical framework for future large-scale explorations of its diversity.
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Affiliation(s)
- Ziguang Deng
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, Shandong Province, China
| | - Wei Yang
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, China
| | - Tongtong Lin
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, China
| | - Yaohai Wang
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, China
| | - Xiaojing Hua
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, China
| | - Xiaoyu Jiang
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, China
| | - Junhao Chen
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, China
| | - Dan Liu
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, China
| | - Zhiqiang Ye
- School of Life Sciences, Central China Normal University, Wuhan, Hubei Province, China
| | - Yu Zhang
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, China
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA
| | - Hongan Long
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, Shandong Province, China
| | - Jiao Pan
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, China
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Seo CW, Yoo S, Cho Y, Kim JS, Steinegger M, Lim YW. FunVIP: Fungal Validation and Identification Pipeline based on phylogenetic analysis. J Microbiol 2025; 63:e2411017. [PMID: 40313148 DOI: 10.71150/jm.2411017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2024] [Accepted: 01/20/2025] [Indexed: 05/03/2025]
Abstract
The increase of sequence data in public nucleotide databases has made DNA sequence-based identification an indispensable tool for fungal identification. However, the large proportion of mislabeled sequence data in public databases leads to frequent misidentifications. Inaccurate identification is causing severe problems, especially for industrial and clinical fungi, and edible mushrooms. Existing species identification pipelines require separate validation of a dataset obtained from public databases containing mislabeled taxonomic identifications. To address this issue, we developed FunVIP, a fully automated phylogeny-based fungal validation and identification pipeline (https://github.com/Changwanseo/FunVIP). FunVIP employs phylogeny-based identification with validation, where the result is achievable only with a query, database, and a single command. FunVIP command comprises nine steps within a workflow: input management, sequence-set organization, alignment, trimming, concatenation, model selection, tree inference, tree interpretation, and report generation. Users may acquire identification results, phylogenetic tree evidence, and reports of conflicts and issues detected in multiple checkpoints during the analysis. The conflicting sample validation performance of FunVIP was demonstrated by re-iterating the manual revision of a fungal genus with a database with mislabeled sequences, Fuscoporia. We also compared the identification performance of FunVIP with BLAST and q2-feature-classifier with two mass double-revised fungal datasets, Sanghuangporus and Aspergillus section Terrei. Therefore, with its automatic validation ability and high identification performance, FunVIP proves to be a highly promising tool for achieving easy and accurate fungal identification.
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Affiliation(s)
- Chang Wan Seo
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Institute of Biodiversity, Seoul National University, Seoul 08826, Republic of Korea
| | - Shinnam Yoo
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Institute of Biodiversity, Seoul National University, Seoul 08826, Republic of Korea
| | - Yoonhee Cho
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Institute of Biodiversity, Seoul National University, Seoul 08826, Republic of Korea
| | - Ji Seon Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Institute of Biodiversity, Seoul National University, Seoul 08826, Republic of Korea
| | - Martin Steinegger
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea
- Artificial Intelligence Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Young Woon Lim
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Institute of Biodiversity, Seoul National University, Seoul 08826, Republic of Korea
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126
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Lan Q, Wu X, Liu Q, Liang Q, He X, Zhu B. Integrating temporal dynamics of both microbial taxonomic and functional characteristics as a tool for forensic time since deposition estimation. Forensic Sci Int 2025; 369:112406. [PMID: 40009954 DOI: 10.1016/j.forsciint.2025.112406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2024] [Revised: 01/28/2025] [Accepted: 02/10/2025] [Indexed: 02/28/2025]
Abstract
Predicting the time since deposition (TsD) of body fluid stain at a crime scene is highly valuable in forensic investigation, as it can connect a DNA-identified stain donor to a crime or estimate the post-mortem interval in forensic case involving cadaver. Previous study has demonstrated the applicability of microbial taxa for TsD prediction. In this proof-of-concept study, we explored the combined use of taxonomic and functional characteristics in human saliva microbiome for TsD prediction. We investigated the potential correlations between the temporal dynamics in microbial communities and the TsD of saliva stains, utilizing the relative abundance of microbial genera, amplicon sequence variants (AsVs), and the metabolic function pathway profiles. The results revealed that changes in the metabolic function pathway profiles of microbial communities could contribute to TsD estimation of the aged saliva stains. We developed ensemble models with multiple heterogeneous algorithms, also combined microbial species and metabolic function pathway profiles for TsD estimation. The TsD prediction model, developed using the relative abundance of the top 50 microbial genera and metabolic functional pathway profiles with the xgboost algorithm, achieved high accuracy (R2 = 0.76, mean absolute error = 6.28 days) in a 60-day deposition. Besides, we further interpreted the model and identified potential biomarkers for TsD estimation of saliva stains. The current study provided the first evidence to explore the potential of using multiple data modalities for predicting the TsD of aged saliva stains, offering valuable insight for forensic investigation.
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Affiliation(s)
- Qiong Lan
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China; Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaolian Wu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Qinglin Liu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Qinglin Liang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Xiaolong He
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Bofeng Zhu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China; Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China.
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127
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Wang X, Ding Y, Zhang X, Feng Y, Li C, Ge Y, Yang Y, Su J, Chu X. The effects of degraded polysaccharides from Acanthopanax senticosus on growth, antioxidant and immune effects in broiler chicks based on intestinal flora. Poult Sci 2025; 104:104933. [PMID: 40010047 PMCID: PMC11910097 DOI: 10.1016/j.psj.2025.104933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2024] [Revised: 02/15/2025] [Accepted: 02/19/2025] [Indexed: 02/28/2025] Open
Abstract
The aim of this study was to evaluate the effect of degraded polysaccharide of Acanthopanax senticosus (ASPS-1) on the immunological effects and appropriate dosage of broiler chicks with a view to developing a new feed additive. For the experimental design, 180 broiler chicks were randomly divided into six groups, ASPS-1 low, medium and high dose groups, undegraded Acanthopanax senticosus polysaccharide (ASPS) low and medium dose groups and blank control group. The drug was administered for 21 consecutive days, and the growth and data of immune organ index and immune factors were recorded on the 7th, 14th and 21st d. Finally, the effect of ASPS-1 on the intestinal flora of broiler chicks was investigated by high-throughput sequencing of the 16S rRNA gene and the correlation between the main flora and intestinal indexes was analyzed, and the function of microbial community was predicted by using PICRUSt2. The results showed that the addition of high dose of ASPS-1 could promote the body weight growth of broiler chicks, had no significant effect on immune organs, significantly promoted the increase of intestinal villi and crypt ratio, and effectively regulated the levels of serum antioxidant factors and immune indexes. Analysis of the intestinal flora showed that ASPS-1H promoted the proliferation of Lactobacillus, Faecalibacterium, Negativibacillus, and Eubacterium and inhibited the colonization of Desulfovibrio and Turicibacter, and that proliferation of Faecalibacterium, Negativibacillus and Eubacterium was associated with the development of intestinal villi. Predictive analysis of PICRUSt2 function indicates that proliferation of Lactobacillus, Faecalibacterium, Negativibacillus and Eubacterium functions through amino acid metabolism, global and overview maps, replication and repair pathways function. In summary, the addition of high doses of ASPS-1 can improve the immunity of broilers and has the potential to be used as a feed additive.
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Affiliation(s)
- Xueyan Wang
- College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, China
| | - Yi Ding
- College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, China
| | - Xueping Zhang
- College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, China
| | - Yichao Feng
- College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, China
| | - Chenglin Li
- College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, China
| | - Yichen Ge
- College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, China
| | - Yaosen Yang
- College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, China
| | - Jianqing Su
- College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, China
| | - Xiuling Chu
- College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, China.
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128
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dos Reis JBA, de Oliveira TMR, Sartori da Silva MRS, Lopes FAC, de Paula AM, Pontes NDC, do Vale HMM. Different Land Use Systems in the Brazilian Cerrado and Their Effects on Soil Bacterial Communities. Microorganisms 2025; 13:804. [PMID: 40284640 PMCID: PMC12029540 DOI: 10.3390/microorganisms13040804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2025] [Revised: 03/20/2025] [Accepted: 03/22/2025] [Indexed: 04/29/2025] Open
Abstract
The effect of agricultural practices on soil bacterial communities is not constant and depends a lot on the climatic context, changes in the soil characteristics, land use, and agricultural strategy. Thus, knowledge about how different land use systems in the Cerrado influence the diversity and taxonomic structure of microbial communities under the same soil type remains limited. In this context, the objective of this work was to analyze and compare the bacterial communities of Cerrado soil under two different land use systems (cover crop and potato cultivation) and in a neighboring native Cerrado area. For this, we used high-throughput amplicon sequencing of 16S rRNA genes (metabarcoding) to characterize the bacterial community at different taxonomic levels in a native Cerrado area, in a potato crop area, and in an area with cover crops. Our data indicated significant impacts on soil physicochemical properties and enzymatic activity, which directly reflect the dynamics of bacterial communities. The three bacterial phyla with the highest relative abundance in the three areas were Proteobacteria, Actinobacteriota, and Acidobacteriota. At the taxonomic class level, small variations were observed among areas, while at the amplicon sequence variant (ASV) level, these variations were more pronounced. The alpha diversity indices showed that the bacterial communities among the areas are rich and diverse. Bray-Curtis and Jaccard distance-based PCoA demonstrated an overlap of bacterial communities present in the cover crop area with the native Cerrado area and separation from the potato cultivation area. The in silico prediction demonstrated that the native Cerrado area presented the highest values of functional diversity of the soil bacterial community compared to the others. Thus, our results provide a holistic view of how different land use systems in the Cerrado can influence the taxonomic and functional diversity of soil bacterial communities.
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Affiliation(s)
| | - Thayssa Monize Rosa de Oliveira
- Centro de Excelência em Bioinsumos (CEBIO), Instituto Federal Goiano, Campus Morrinhos, Morrinhos 75650-000, GO, Brazil; (T.M.R.d.O.); (N.d.C.P.)
| | | | | | | | - Nadson de Carvalho Pontes
- Centro de Excelência em Bioinsumos (CEBIO), Instituto Federal Goiano, Campus Morrinhos, Morrinhos 75650-000, GO, Brazil; (T.M.R.d.O.); (N.d.C.P.)
| | - Helson Mario Martins do Vale
- University of Brasilia, Institute of Biological Sciences, Brasília 70910-900, DF, Brazil; (J.B.A.d.R.); (M.R.S.S.d.S.)
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129
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Speer KA, Víquez‐R L, Frick WF, Ibarra A, Simmons NB, Dittmar K, Calderón RS, Preciado R, Medellín R, Tschapka M, Sommer S, Perkins SL. Comparative Community Ecology Reveals Conserved Ectoparasite Microbiomes Amidst Variable Host and Environment Microbiomes. Ecol Evol 2025; 15:e71120. [PMID: 40177692 PMCID: PMC11962207 DOI: 10.1002/ece3.71120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2024] [Revised: 02/15/2025] [Accepted: 02/26/2025] [Indexed: 04/05/2025] Open
Abstract
The microbiome-the community of microorganisms that is associated with an individual animal-has been an important driver of insect biodiversity globally, enabling insects to specialize in narrow, nutrient-deficient diets. The importance of maternally inherited, obligate bacterial endosymbionts in provisioning nutrients missing from these narrow dietary niches has been well studied in insects. However, we know comparatively little about the processes that dictate the composition of non-maternally inherited bacteria in insect microbiomes, despite the importance of these bacteria in insect health, fitness, and vector competence. Here, we used two species of obligate insect ectoparasites of bats, the bat flies (Streblidae) Trichobius sphaeronotus and Nycterophilia coxata, to examine whether the microbiome, beyond obligate bacterial endosymbionts, is conserved or variable across geographic space, between ectoparasite species, or covaries with the external microbiome of their bat hosts or the cave environment. Our results indicate that ectoparasite microbiomes are highly conserved and specific to ectoparasite species, despite these species feeding on the blood of the same bat individuals in some cases. In contrast, we found high geographic variation in the fur microbiome of host bats and that the bat fur microbiome mimics the cave microbiomes. This research suggests that there is a constraint on blood-feeding insect ectoparasites to maintain a specific microbiome distinct from their host and the environment, potentially to meet their nutritional needs. Given that many of these bacteria are not known to be maternally inherited, this research lays the foundation for future examinations of how blood-feeding arthropods acquire and maintain bacteria in their microbiomes.
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Affiliation(s)
- Kelly A. Speer
- Department of Biological SciencesNorthern Arizona UniversityFlagstaffArizonaUSA
- Pathogen and Microbiome InstituteNorthern Arizona UniversityFlagstaffArizonaUSA
| | - Luis Víquez‐R
- Department of BiologyBucknell UniversityLewisburgPennsylvaniaUSA
- Institute of Evolutionary Ecology and Conservation GeneticsUniversität UlmUlmGermany
| | - Winifred F. Frick
- Department of Ecology and Evolutionary BiologyUniversity of California Santa CruzSanta CruzCaliforniaUSA
- Bat Conservation InternationalAustinTexasUSA
| | - Ana Ibarra
- Bat Conservation InternationalAustinTexasUSA
- Laboratorio de Ecología y Conservación de Vertebrados TerrestresUniversidad Nacional Autónoma de MéxicoMexico CityMexico
| | - Nancy B. Simmons
- Department of MammalogyAmerican Museum of Natural HistoryNew YorkNew YorkUSA
| | | | | | - Raisa Preciado
- Facultad Interdisciplinaria de Ciencias Biológicas y de SaludUniversidad de SonoraHermosilloSonoraMexico
| | - Rodrigo Medellín
- Laboratorio de Ecología y Conservación de Vertebrados TerrestresUniversidad Nacional Autónoma de MéxicoMexico CityMexico
| | - Marco Tschapka
- Institute of Evolutionary Ecology and Conservation GeneticsUniversität UlmUlmGermany
| | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation GeneticsUniversität UlmUlmGermany
| | - Susan L. Perkins
- City College of New YorkCity University of New YorkNew YorkNew YorkUSA
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130
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Pastor-López EJ, Escolà Casas M, Hellman D, Müller JA, Matamoros V. Impact of riverbed renaturalization on the attenuation of antibiotics and antimicrobial resistance in wastewater effluent-dominated streams. ENVIRONMENTAL RESEARCH 2025; 270:120910. [PMID: 39880113 DOI: 10.1016/j.envres.2025.120910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2024] [Revised: 01/17/2025] [Accepted: 01/19/2025] [Indexed: 01/31/2025]
Abstract
Mediterranean streams contain substantial proportions of wastewater treatment plant effluent, occasionally constituting the entire water flow. Here, we analysed the seasonal occurrence of 23 antibiotics (AB) and antimicrobial resistance (AMR) by tracking 3 marker genes and bacterial community dynamics in two wastewater effluent-dominated streams. One stream was renaturalized with meanders and vegetation, while the other was linear and had a low vegetation density. The concentration of ABs in the effluents ranged from 33 to 1313 ng·L-1 during summer and 4 to 2337 ng·L-1 during winter. The attenuation of ABs 3.5 km downstream varied depending on the compound, ranging from 42 to 88%. The half-lives of ABs obtained for the streams were 0.2-4.1 h in summer and 0.6-12.6 h in winter. Most ABs had a half-life of <5 h, except sulfamethoxazole, acetyl-sulfamethoxazole, and trimethoprim. The vegetated stream exhibited a higher attenuation of ABs than the unaltered stream (88% vs. 67% on average), while also showing lower half-life values (on average 1.3 vs. 3.8 h). The bacterial community profiles in both streams were typical of effluents, with greater longitudinal dynamics in the vegetated stream during summer than in the other samplings. Similarly, AMR indicator genes decreased most in the vegetated stream during summer (0.8-1.1 log units). The ecotoxicological risk and the potential microbial risk selection values downstream at 3.5 km were reduced by > 45%. Overall, the results suggest that vegetation and meanders play an important role in the in-stream attenuation of ABs and AMRs.
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Affiliation(s)
- Edward J Pastor-López
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona, 18-26, 08034, Barcelona, Spain
| | - Mònica Escolà Casas
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona, 18-26, 08034, Barcelona, Spain
| | - Dominik Hellman
- Institute for Biological Interfaces (IBG-5), Karlsruhe Institute of Technology, 76344, Eggenstein-Leopoldshafen, Germany
| | - Jochen A Müller
- Institute for Biological Interfaces (IBG-5), Karlsruhe Institute of Technology, 76344, Eggenstein-Leopoldshafen, Germany
| | - Víctor Matamoros
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona, 18-26, 08034, Barcelona, Spain.
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131
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McHugh RE, Rooney LM, Mark DR, Wale KR, Clapperton M, McConnell G, Hoskisson PA, Douce GR, Roe AJ. Evaluating the protective effects of Aurodox in a murine model of Shiga toxin-producing Escherichia coli. NPJ ANTIMICROBIALS AND RESISTANCE 2025; 3:23. [PMID: 40169888 PMCID: PMC11962119 DOI: 10.1038/s44259-025-00094-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2024] [Accepted: 03/14/2025] [Indexed: 04/03/2025]
Abstract
Shiga Toxin-Producing E. coli (STEC) are a group of acute small intestine pathogens responsible for foodborne outbreaks of bloody diarrhoea. The expression of Shiga toxins (Stx) carried by STEC can initiate Haemolytic Uremic Syndrome (HUS), a major cause of acute renal failure in children. Here, we investigate the anti-virulence potential of Aurodox - a natural product of Streptomyces goldiniensis. Previously, we have shown that Aurodox downregulates the expression of the T3SS, inhibiting epithelial cell colonisation in vitro. Here, we use the Citrobacter rodentium DBS770 (Cr Stx2dact) model of STEC infection to demonstrate that Aurodox protects mice against Citrobacter rodentium-associated colonic hyperplasia and Stx-mediated renal injury. Given antibiotic-associated dysbiosis of the gut is associated with inflammation and the emergence of opportunistic pathogens, we examined the effect of Aurodox on the faecal bacteriome. We show that although the microbial community is altered following Aurodox treatment, changes are distinct from those associated with traditional antibiotic therapies.
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Affiliation(s)
- Rebecca E McHugh
- School of Infection and Immunity, University of Glasgow, Glasgow, UK
| | - Liam M Rooney
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, UK
- School of Infection and Immunity, University of Glasgow, Glasgow, UK
| | - David R Mark
- School of Infection and Immunity, University of Glasgow, Glasgow, UK
| | - Kabo R Wale
- School of Infection and Immunity, University of Glasgow, Glasgow, UK
- Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Megan Clapperton
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, UK
| | - Gail McConnell
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, UK
| | - Paul A Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, UK
| | - Gillian R Douce
- School of Infection and Immunity, University of Glasgow, Glasgow, UK
| | - Andrew J Roe
- School of Infection and Immunity, University of Glasgow, Glasgow, UK.
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132
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Thakur BK, Malaise Y, Choudhury SR, Neustaeter A, Turpin W, Streutker C, Copeland J, Wong EOY, Navarre WW, Guttman DS, Jobin C, Croitoru K, Martin A. Dietary fibre counters the oncogenic potential of colibactin-producing Escherichia coli in colorectal cancer. Nat Microbiol 2025; 10:855-870. [PMID: 40033140 DOI: 10.1038/s41564-025-01938-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Accepted: 01/14/2025] [Indexed: 03/05/2025]
Abstract
Diet, microbiome, inflammation and host genetics have been linked to colorectal cancer development; however, it is not clear whether and how these factors interact to promote carcinogenesis. Here we used Il10-/- mice colonized with bacteria previously associated with colorectal cancer: enterotoxigenic Bacteroides fragilis, Helicobacter hepaticus or colibactin-producing (polyketide synthase-positive (pks+)) Escherichia coli and fed either a low-carbohydrate (LC) diet deficient in soluble fibre, a high-fat and high-sugar diet, or a normal chow diet. Colonic polyposis was increased in mice colonized with pks+ E. coli and fed the LC diet. Mechanistically, mucosal inflammation was increased in the LC-diet-fed mice, leading to diminished colonic PPAR-γ signalling and increased luminal nitrate levels. This promoted both pks+ E. coli growth and colibactin-induced DNA damage. PPAR-γ agonists or supplementation with dietary soluble fibre in the form of inulin reverted inflammatory and polyposis phenotypes. The pks+ E. coli also induced more polyps in mismatch-repair-deficient mice by inducing a senescence-associated secretory phenotype. Moreover, oncogenic effects were further potentiated by inflammatory triggers in the mismatch-repair-deficient model. These data reveal that diet and host genetics influence the oncogenic potential of a common bacterium.
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Affiliation(s)
| | - Yann Malaise
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | | | - Anna Neustaeter
- Division of Gastroenterology, Department of Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Williams Turpin
- Division of Gastroenterology, Department of Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Catherine Streutker
- Department of Laboratory Medicine, Unity Health Toronto, Toronto, Ontario, Canada
| | - Julia Copeland
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario, Canada
| | - Erin O Y Wong
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - William W Navarre
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - David S Guttman
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario, Canada
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Christian Jobin
- Department of Infectious Diseases and Pathology, University of Florida College of Veterinary Medicine, Gainesville, FL, USA
| | - Kenneth Croitoru
- Division of Gastroenterology, Department of Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Alberto Martin
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada.
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133
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Kovynev A, Charchuta MM, Begtašević A, Ducarmon QR, Rensen PCN, Schönke M. Combination of dietary fiber and exercise training improves fat loss in mice but does not ameliorate MASLD more than exercise alone. Am J Physiol Gastrointest Liver Physiol 2025; 328:G399-G410. [PMID: 40033967 DOI: 10.1152/ajpgi.00317.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2024] [Revised: 01/02/2025] [Accepted: 02/20/2025] [Indexed: 03/05/2025]
Abstract
Lifestyle interventions, such as diet and exercise, are currently the main therapies against metabolic dysfunction-associated steatotic liver disease (MASLD). However, not much is known about the combined impact of fiber and exercise on the modulation of gut-liver axis and MASLD amelioration. Here, we studied the impact of the combination of exercise training and a fiber-rich diet on the amelioration of MASLD. Male APOE*3-Leiden.CETP mice were fed a high-fat high-cholesterol diet with or without the addition of fiber (10% inulin) and exercise trained on a treadmill, or remained sedentary. Exercise training and fiber supplementation reduced fat mass gain and lowered plasma glucose levels. Only the combination treatment, however, induced fat loss and decreased plasma triglyceride and cholesterol levels compared with sedentary control mice. Exercise training with and without the addition of fiber had a similar ameliorating effect on the MASLD score. Only exercise without fiber decreased the hepatic expression of inflammatory markers. Fiber diet was mainly responsible for remodeling the gut microbial composition, with an increase in the relative abundance of the short-chain fatty acid (SCFA)-producing genera Anaerostipes and Muribaculaceae, whereas, surprisingly, exercise training alone and with fiber resulted in the highest increase of SCFA production. Overall, the combination of exercise training and dietary fiber decreases fat mass and improves glucose and lipid homeostasis but does not have an additional synergistic positive effect on liver health compared with exercise training alone.NEW & NOTEWORTHY The combination of dietary fiber intake and exercise training has a synergetic beneficial effect on the metabolic health, resulting in fat loss, lowered blood glucose, and lowered plasma lipid levels in mice with steatotic liver disease. However, fiber supplementation, despite a positive remodulation of the gut-liver axis, does not have an additional positive effect on liver health compared with exercise training alone.
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Affiliation(s)
- Artemiy Kovynev
- Division of Endocrinology, Department of Medicine, Leiden University Medical Center, Leiden, The Netherlands
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Mikołaj M Charchuta
- Division of Endocrinology, Department of Medicine, Leiden University Medical Center, Leiden, The Netherlands
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Amina Begtašević
- Division of Endocrinology, Department of Medicine, Leiden University Medical Center, Leiden, The Netherlands
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Quinten R Ducarmon
- Leiden University Center for Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Patrick C N Rensen
- Division of Endocrinology, Department of Medicine, Leiden University Medical Center, Leiden, The Netherlands
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Milena Schönke
- Division of Endocrinology, Department of Medicine, Leiden University Medical Center, Leiden, The Netherlands
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
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134
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Ding J, Gou W, Ma M, Cui Y, Lyu B, Xu J, Wang Z, Zhao Q, Li Y, Hou W. Investigation of the fingerprint-activity relationship of Tremella fuciformis polysaccharides and its mitigating effect on radiation-induced intestinal injury. Int J Biol Macromol 2025; 304:140849. [PMID: 39938826 DOI: 10.1016/j.ijbiomac.2025.140849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2024] [Revised: 01/17/2025] [Accepted: 02/08/2025] [Indexed: 02/14/2025]
Abstract
The aim of this study was to conduct a comprehensive analysis of the relationship between the fingerprint of Tremella fuciformis polysaccharides (TFPs) sourced from China and their bioactivities, with an emphasis on identifying the most bioactive TFP variety that significantly mitigated radiation-induced intestinal injury (RIII). Firstly, the multi-fingerprints we developed indicated that TFPs were classified as acidic, primarily consisting of mannose, rhamnose, glucuronic acid, glucose, xylose, and fucose, with average molecular weight (Mw) ranging from 1.65 × 103 to 2.50 × 103 kDa. Subsequently, in vitro activity evaluations demonstrated variability in the antioxidant activities and the inhibitory effects on cancer cell proliferation among TFPs. Multiple linear regression analysis indicated a significant correlation between monosaccharide composition of TFPs and their bioactivity, whereas Mw did not exhibit a similar relationship. Notably, TFP sourced from Zhenjinhui (Gutian, Fujian) (i.e., TFP-2) and Shengkuo (Tongjiang, Sichuan) (i.e., TFP-23) exhibited the most significant bioactivities, both effectively mitigating RIII in mice, with TFP-23 proving to be more effective. Further investigations indicated that TFP-23 provided radioprotective benefits by rectifying RIII-induced dysbiosis of intestinal microbiota and increasing probiotic abundance. Consequently, this study not only clarifies the fingerprint-activity relationship of TFPs but also promotes the potential of TFP-23 as innovative agents for radiation protection.
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Affiliation(s)
- Juanjuan Ding
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin 300192, PR China
| | - Wenfeng Gou
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin 300192, PR China
| | - Mingwei Ma
- Fullbin Biotechnology (Tianjin) Co., Ltd., PR China
| | - Yating Cui
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin 300192, PR China
| | - Bohai Lyu
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China
| | - Jingfei Xu
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin 300192, PR China
| | - Zhiyun Wang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin 300192, PR China
| | - Qian Zhao
- Nankai Wangdingdi Hospital, Tianjin 300191, PR China
| | - Yiliang Li
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin 300192, PR China.
| | - Wenbin Hou
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin 300192, PR China.
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Skičková Š, Kratou M, Svobodová K, Maitre A, Abuin-Denis L, Wu-Chuang A, Obregón D, Said MB, Majláthová V, Krejčí A, Cabezas-Cruz A. Functional redundancy and niche specialization in honeybee and Varroa microbiomes. Int Microbiol 2025; 28:795-810. [PMID: 39172274 DOI: 10.1007/s10123-024-00582-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 08/07/2024] [Accepted: 08/13/2024] [Indexed: 08/23/2024]
Abstract
The honeybee (Apis mellifera) is a key pollinator critical to global agriculture, facing threats from various stressors, including the ectoparasitic Varroa mite (Varroa destructor). Previous studies have identified shared bacteria between Varroa mites and honeybees, yet it remains unclear if these bacteria assemble similarly in both species. This study builds on existing knowledge by investigating co-occurrence patterns in the microbiomes of both Varroa mites and honeybees, shedding light on potential interactions. Leveraging 16S rRNA datasets, we conducted co-occurrence network analyses, explored Core Association Networks (CAN) and assess network robustness. Comparative network analyses revealed structural differences between honeybee and mite microbiomes, along with shared core features and microbial motifs. The mite network exhibited lower robustness, suggesting less resistance to taxa extension compared to honeybees. Furthermore, analyses of predicted functional profiling and taxa contribution revealed that common central pathways in the metabolic networks have different taxa contributing to Varroa mites and honeybee microbiomes. The results show that while both microbial systems exhibit functional redundancy, in which different taxa contribute to the functional stability and resilience of the ecosystem, there is evidence for niche specialization resulting in unique contributions to specific pathways in each part of this host-parasite system. The specificity of taxa contribution to key pathways offers targeted approaches to Varroa microbiome management and preserving honeybee microbiome. Our findings provide valuable insights into microbial interactions, aiding farmers and beekeepers in maintaining healthy and resilient bee colonies amid increasing Varroa mite infestations.
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Affiliation(s)
- Štefánia Skičková
- Pavol Jozef Šafárik University in Košice, Faculty of Science, Institute of Biology and Ecology, Department of Animal Physiology, Košice, 04181, Slovakia.
| | - Myriam Kratou
- Laboratory of Microbiology, National School of Veterinary Medicine of Sidi Thabet, University of Manouba, 2010, Manouba, Tunisia
| | - Karolína Svobodová
- University of South Bohemia, Faculty of Science, České Budějovice, 37005, Czech Republic
| | - Apolline Maitre
- ANSES, INRAE, École Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, 94700, Maisons-Alfort, France
- INRAE, UR 0045 Laboratoire de Recherches Sur Le Développement de L'Elevage (SELMET-LRDE), 20250, Corte, France
- EA 7310, Laboratoire de Virologie, Université de Corse, 20250, Corte, France
| | - Lianet Abuin-Denis
- ANSES, INRAE, École Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, 94700, Maisons-Alfort, France
- Animal Biotechnology Department, Center for Genetic Engineering and Biotechnology, Avenue 31 Between 158 and 190, P.O. Box 6162, 10600, Havana, Cuba
| | - Alejandra Wu-Chuang
- ANSES, INRAE, École Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, 94700, Maisons-Alfort, France
| | - Dasiel Obregón
- School of Environmental Sciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Mourad Ben Said
- Laboratory of Microbiology, National School of Veterinary Medicine of Sidi Thabet, University of Manouba, 2010, Manouba, Tunisia
- Department of Basic Sciences, Higher Institute of Biotechnology of Sidi Thabet, University of Manouba, 2010, Manouba, Tunisia
| | - Viktória Majláthová
- Pavol Jozef Šafárik University in Košice, Faculty of Science, Institute of Biology and Ecology, Department of Animal Physiology, Košice, 04181, Slovakia
| | - Alena Krejčí
- University of South Bohemia, Faculty of Science, České Budějovice, 37005, Czech Republic
- Czech Academy of Sciences, Biology Centre, Institute of Entomology, České Budějovice, 37005, Czech Republic
| | - Alejandro Cabezas-Cruz
- ANSES, INRAE, École Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, 94700, Maisons-Alfort, France.
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Shahmohamadloo RS, Gabidulin AR, Andrews ER, Fryxell JM, Rudman SM. A test for microbiome-mediated rescue via host phenotypic plasticity in Daphnia. Proc Biol Sci 2025; 292:20250365. [PMID: 40199359 PMCID: PMC11978444 DOI: 10.1098/rspb.2025.0365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2025] [Revised: 03/14/2025] [Accepted: 03/14/2025] [Indexed: 04/10/2025] Open
Abstract
Phenotypic plasticity is a primary mechanism by which organismal phenotypes shift in response to the environment. Host-associated microbiomes often change considerably in response to environmental variation, and these shifts could facilitate host phenotypic plasticity, adaptation, or rescue populations from extinction. However, it is unclear whether changes in microbiome composition contribute to host phenotypic plasticity, limiting our knowledge of the underlying mechanisms of plasticity and, ultimately, the fate of populations inhabiting changing environments. In this study, we examined the phenotypic responses and microbiome composition of 20 genetically distinct Daphnia magna genotypes exposed to non-toxic and toxic diets containing Microcystis, a cosmopolitan cyanobacterium and common stressor for Daphnia. Daphnia exhibited significant plasticity in survival, reproduction and population growth rates upon exposure to Microcystis. However, the effects of Microcystis exposure on the Daphnia microbiome were limited, with the primary effect being differences in abundance observed across five bacterial families. Moreover, there was no significant correlation between the magnitude of microbiome shifts and host phenotypic plasticity. Our results suggest that microbiome composition played a negligible role in driving host phenotypic plasticity or microbiome-mediated rescue.
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Affiliation(s)
| | - Amir R. Gabidulin
- School of Biological Sciences, Washington State University, Vancouver, WA, USA
| | - Ellie R. Andrews
- School of Biological Sciences, Washington State University, Vancouver, WA, USA
| | - John M. Fryxell
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Seth M. Rudman
- School of Biological Sciences, Washington State University, Vancouver, WA, USA
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Freitas JA, Nehmi Filho V, Santamarina AB, Murata GM, Franco LAM, Fonseca JV, Martins RC, Souza GA, Benicio G, Sabbag IM, de Souza EA, Otoch JP, Pessoa AFM. Nutraceutical supplement slim reshaped colon histomorphology and reduces Mucispirillum schaedleri in obese mice. Front Microbiol 2025; 16:1494994. [PMID: 40236479 PMCID: PMC11997693 DOI: 10.3389/fmicb.2025.1494994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2024] [Accepted: 02/28/2025] [Indexed: 04/17/2025] Open
Abstract
Introduction Bioactive compounds and whole foods have emerged as promising interventions to address gut microbiota dysbiosis linked to obesity. Compounds such as berberine and coenzyme Q10 are well-recognized for their roles in managing metabolic syndrome and exerting antioxidant effects, while beet pulp, rich in fiber and antioxidants, enhances gut health through additional prebiotic benefits. Methods This study evaluated the effects of a nutraceutical supplement, Slim, on the modulation of gut microbiota in obese mice induced by a high-fat diet. Results Our results demonstrated that Slim supplementation significantly improved lipid metabolism, reshaped colon histomorphology, and decreased levels of Mucispirillum schaedleri, which were correlated with VLDL-c and triglycerides. Discussion We suggest these effects are driven by a duplibiotic effect, resulting from the synergistic action of the bioactive compounds.
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Affiliation(s)
- Jessica Alves Freitas
- Laboratório de Produtos e Derivados Naturais, Laboratório de Investigação Médica-26 (LIM-26), Departamento de Cirurgia, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
- Pesquisa e Desenvolvimento Efeom Nutrição S/A, São Paulo, SP, Brazil
| | - Victor Nehmi Filho
- Laboratório de Produtos e Derivados Naturais, Laboratório de Investigação Médica-26 (LIM-26), Departamento de Cirurgia, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
- Pesquisa e Desenvolvimento Efeom Nutrição S/A, São Paulo, SP, Brazil
| | - Aline Boveto Santamarina
- Laboratório de Produtos e Derivados Naturais, Laboratório de Investigação Médica-26 (LIM-26), Departamento de Cirurgia, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
- Pesquisa e Desenvolvimento Efeom Nutrição S/A, São Paulo, SP, Brazil
| | - Gilson Masahiro Murata
- Universidade de São Paulo Faculdade de Medicina da Universidade de São Paulo, Departamento de Clínica Médica, Laboratório de Nefrologia (LIM-29), São Paulo, SP, Brazil
| | - Lucas Augusto Moyses Franco
- Universidade de São Paulo Instituto de Medicina Tropical de São Paulo, Departamento de Doenças Infecciosas e Parasitárias, Laboratório de Parasitologia Médica (LIM-46), São Paulo, SP, Brazil
| | - Joyce Vanessa Fonseca
- Universidade de São Paulo Instituto de Medicina Tropical de São Paulo, Departamento de Doenças Infecciosas e Parasitárias, Laboratório de Investigação Médica em Protozoologia, Bacteriologia e Resistência Antimicrobiana (LIM-49), São Paulo, SP, Brazil
| | - Roberta Cristina Martins
- Universidade de São Paulo Instituto de Medicina Tropical de São Paulo, Departamento de Doenças Infecciosas e Parasitárias, Laboratório de Parasitologia Médica (LIM-46), São Paulo, SP, Brazil
| | - Gabriele Alves Souza
- Universidade de São Paulo Faculdade de Medicina da Universidade de São Paulo, Departamento de Patologia, Laboratório de Neurociência (LIM-01), São Paulo, SP, Brazil
| | - Gabriela Benicio
- Universidade de São Paulo Faculdade de Medicina da Universidade de São Paulo, Departamento de Patologia, Laboratório de Neurociência (LIM-01), São Paulo, SP, Brazil
| | - Isabella Mirandez Sabbag
- Universidade de São Paulo Faculdade de Medicina da Universidade de São Paulo, Departamento de Patologia, Laboratório de Neurociência (LIM-01), São Paulo, SP, Brazil
| | - Esther Alves de Souza
- Laboratório de Produtos e Derivados Naturais, Laboratório de Investigação Médica-26 (LIM-26), Departamento de Cirurgia, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
- Pesquisa e Desenvolvimento Efeom Nutrição S/A, São Paulo, SP, Brazil
| | - José Pinhata Otoch
- Laboratório de Produtos e Derivados Naturais, Laboratório de Investigação Médica-26 (LIM-26), Departamento de Cirurgia, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
- Pesquisa e Desenvolvimento Efeom Nutrição S/A, São Paulo, SP, Brazil
- Hospital Universitário da Universidade de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Ana Flávia Marçal Pessoa
- Laboratório de Produtos e Derivados Naturais, Laboratório de Investigação Médica-26 (LIM-26), Departamento de Cirurgia, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
- Universidade de São Paulo Instituto de Medicina Tropical de São Paulo, Departamento de Doenças Infecciosas e Parasitárias, Laboratório de Parasitologia Médica (LIM-46), São Paulo, SP, Brazil
- Instituto Botânio, São Paulo, Brazil
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138
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Sweeney CJ, Bottoms M, Kaushik R, Aderjan E, Sherborne N. Functional versus compositional tests in the risk assessment of the impacts of pesticides on the soil microbiome. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2025; 44:1120-1133. [PMID: 39987504 DOI: 10.1093/etojnl/vgaf012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2024] [Revised: 12/18/2024] [Accepted: 12/19/2024] [Indexed: 02/25/2025]
Abstract
The Organisation of Economic Co-operation and Development (OECD) 216 nitrogen transformation test is used to understand the impacts of plant protection products (PPPs) on the soil microbiome. However, there is significant interest in developing the European PPP risk assessment to include new technologies such as amplicon sequencing to assess impacts on soil microbial community composition and diversity. We have little understanding of how to generate endpoints from amplicon sequencing data sets, their robustness, and whether they provide an appropriate level of protection to the soil microbiome. Our study addresses this key knowledge gap. We conducted a dose-response OECD 216 study with two chemicals, nitrapyrin and streptomycin, and calculated traditional functional endpoints, in accordance with the OECD 216 guideline, and used amplicon sequencing techniques to generate a range of endpoints based on soil bacterial diversity, richness, dissimilarity from the control, species sensitivity distributions, and threshold indicator analysis. We show it is possible to generate a range of endpoints from amplicon sequencing data sets; however, these endpoints varied significantly based on the calculation method, with up to a 101-fold difference between the least and most sensitive endpoints. Additionally, the relative sensitivity of these endpoints compared to the currently used functional OECD 216 metrics was compound dependent, with many endpoint calculation methods unable to detect the impacts of nitrapyrin on the soil microbiome at concentrations deemed ecotoxicologically relevant by OECD 216. Our study shows amplicon sequencing methods to study soil microbial ecotoxicology did not perform consistently and reliably when considering both nitrapyrin and streptomycin treatments and in many cases did not consistently provide an enhanced degree of protection over the functional OECD 216 assessments already integrated into the PPP risk assessment.
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Affiliation(s)
- Christopher J Sweeney
- Product Safety, Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire, United Kingdom
| | - Melanie Bottoms
- Product Safety, Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire, United Kingdom
| | - Rishabh Kaushik
- Product Safety, Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire, United Kingdom
| | - Eva Aderjan
- Eurofins Agroscience Services Ecotox GmbH, Niefern-Öschelbronn, Germany
| | - Neil Sherborne
- Product Safety, Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire, United Kingdom
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Li J, Sun W, Cao Y, Wu J, Duan L, Zhang M, Luo X, Deng Q, Peng Z, Mou X, Li W, Wang P. Increased temperature enhances microbial-mediated lignin decomposition in river sediment. MICROBIOME 2025; 13:89. [PMID: 40170118 PMCID: PMC11959967 DOI: 10.1186/s40168-025-02076-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/04/2025] [Indexed: 04/03/2025]
Abstract
BACKGROUND Lignin, as the most abundant recalcitrant organic carbon in terrestrial ecosystems, plays a crucial role in the Earth's carbon cycle. After lignin entering aquatic environments, portion of it tends to accumulate in sediments, forming a stable carbon relatively reservoir. However, the increasing temperature caused by human activities may impact microbial-mediated lignin decomposition, thereby affecting sedimentary carbon reservoirs. Therefore, revealing how temperature affects microbial-mediated lignin decomposition in river sediment, a topic that remains elusive, is essential for comprehending the feedbacks between river carbon reservoirs and climate. To address this, we conducted stable isotope probing of river surface sediment using 13C-lignin and 13C-vanillin, and utilized a series of techniques, including CO2 production analysis, 16S rRNA gene amplicon sequencing, metagenomics, and metatranscriptomics, to identify the lignin-decomposing microbes and the effects of temperature on microbial-mediated lignin decomposition. RESULTS We found that elevated temperatures not only increased the total sediment respiration (total CO2) and the CO2 emissions from lignin/vanillin decomposition, but also enhanced priming effects. The 13C-labled taxa, including Burkholderiales, Sphingomonadales, and Pseudomonadales, were identified as the main potential lignin/vanillin decomposers, and their abundances and activity significantly increased as temperature increased. Furthermore, we observed that increasing temperature significantly increased the activity of lignin decomposing pathways, including β-aryl ether fragments and 4,5-PDOG pathway. Additionally, as temperature increases, the transcriptional abundances of other carbon cycling related genes, such as pulA (starch decomposition) and xyla (hemicellulose decomposition), also exhibited increasing trends. Overall, our study elucidated the potential lignin-decomposing microbes and pathways in river sediment and their responses to temperature increasing. CONCLUSIONS Our study demonstrated that the temperature increasing can increase the rate of lignin/vanillin decomposition via affecting the activity of lignin-decomposing microbes. This finding indicates that the ongoing intensification of global warming may enhance the decomposition of recalcitrant organic carbon in river sediment, thereby impacting global carbon cycling. Video Abstract.
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Affiliation(s)
- Jialing Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Environmental Science and Engineering, School of Life Sciences, School of Ecology, Sun Yat-Sen University, Guangzhou, Guangdong, 510275, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Weimin Sun
- Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Yingjie Cao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Environmental Science and Engineering, School of Life Sciences, School of Ecology, Sun Yat-Sen University, Guangzhou, Guangdong, 510275, China
| | - Jiaxue Wu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Environmental Science and Engineering, School of Life Sciences, School of Ecology, Sun Yat-Sen University, Guangzhou, Guangdong, 510275, China
| | - Li Duan
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Environmental Science and Engineering, School of Life Sciences, School of Ecology, Sun Yat-Sen University, Guangzhou, Guangdong, 510275, China
| | - Miaomiao Zhang
- Key Laboratory of Water Quality and Conservation in the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Xiaoqing Luo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Environmental Science and Engineering, School of Life Sciences, School of Ecology, Sun Yat-Sen University, Guangzhou, Guangdong, 510275, China
| | - Qiqi Deng
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Environmental Science and Engineering, School of Life Sciences, School of Ecology, Sun Yat-Sen University, Guangzhou, Guangdong, 510275, China
| | - Ziqi Peng
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Environmental Science and Engineering, School of Life Sciences, School of Ecology, Sun Yat-Sen University, Guangzhou, Guangdong, 510275, China
| | - Xiaozhen Mou
- Department of Biological Sciences, Kent State University, Kent, OH, 44242, USA
| | - Wenjun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Environmental Science and Engineering, School of Life Sciences, School of Ecology, Sun Yat-Sen University, Guangzhou, Guangdong, 510275, China.
| | - Pandeng Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Environmental Science and Engineering, School of Life Sciences, School of Ecology, Sun Yat-Sen University, Guangzhou, Guangdong, 510275, China.
- School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518055, China.
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140
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Zhao M, Xiong S, Du T, Xu X, Li H, Zhang L, Xu Y, Wei T, Ren H, Xiong T, Xie M. Analysis of the quality and bacterial composition of spicy cabbage between Liaoning and Yanbian in northeastern China based on flavoromics and amplicon sequencing. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2025. [PMID: 40164994 DOI: 10.1002/jsfa.14250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2025] [Revised: 03/10/2025] [Accepted: 03/13/2025] [Indexed: 04/02/2025]
Abstract
BACKGROUND Chinese spicy cabbage (CSC) is a famous traditional fermented vegetable widely consumed in northeast China. However, the differences in characteristics between Liaoning spicy cabbage (LNSC) and Yanbian spicy cabbage (YBSC), as well as the correlation between flavor attributes and microbiota remain unclear. This study clearly delineated the characteristics and correlations of ingredients, aroma characteristics and microbial communities between LNSC and YBSC. RESULTS Metabolomic analysis revealed distinct compositional differences in both volatile and non-volatile metabolites between LNSC and YBSC. Through relative odor activity value analysis, 17 and 14 key flavor compounds were identified as characteristic components in LNSC and YBSC, respectively. Amplicon sequencing demonstrated significant regional variations in the bacterial community structure of CSC. Spearman correlation analysis demonstrated strong correlations between 20 bacteria and 11 free amino acids, 22 volatile flavor compounds. CONCLUSION This study systematically compared the quality characteristics between LNSC and YBSC, providing fundamental data for the evaluation of spicy cabbage and fermented food products. © 2025 Society of Chemical Industry.
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Affiliation(s)
- Mingwei Zhao
- State Key Laboratory of Food Science & Resources, Nanchang University, Nanchang, China
- School of Food Science & Technology, Nanchang University, Nanchang, China
| | - Shijin Xiong
- State Key Laboratory of Food Science & Resources, Nanchang University, Nanchang, China
- School of Food Science & Technology, Nanchang University, Nanchang, China
| | - Tonghao Du
- State Key Laboratory of Food Science & Resources, Nanchang University, Nanchang, China
- School of Food Science & Technology, Nanchang University, Nanchang, China
| | - Xiaoyan Xu
- State Key Laboratory of Food Science & Resources, Nanchang University, Nanchang, China
- School of Food Science & Technology, Nanchang University, Nanchang, China
| | - Huiyu Li
- State Key Laboratory of Food Science & Resources, Nanchang University, Nanchang, China
- School of Food Science & Technology, Nanchang University, Nanchang, China
| | - Linli Zhang
- State Key Laboratory of Food Science & Resources, Nanchang University, Nanchang, China
- School of Food Science & Technology, Nanchang University, Nanchang, China
| | - Yazhou Xu
- State Key Laboratory of Food Science & Resources, Nanchang University, Nanchang, China
- School of Food Science & Technology, Nanchang University, Nanchang, China
| | - Tao Wei
- State Key Laboratory of Food Science & Resources, Nanchang University, Nanchang, China
- School of Food Science & Technology, Nanchang University, Nanchang, China
| | - Hongbing Ren
- Yunnan Key Laboratory of Fermented Vegetables, Honghe, China
| | - Tao Xiong
- State Key Laboratory of Food Science & Resources, Nanchang University, Nanchang, China
- School of Food Science & Technology, Nanchang University, Nanchang, China
| | - Mingyong Xie
- State Key Laboratory of Food Science & Resources, Nanchang University, Nanchang, China
- School of Food Science & Technology, Nanchang University, Nanchang, China
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Wang P, Li H, Zhang X, Wang X, Sun W, Zhang X, Chi B, Go Y, Chan XHF, Wu J, Huang Q. Microecology in vitro model replicates the human skin microbiome interactions. Nat Commun 2025; 16:3085. [PMID: 40164644 PMCID: PMC11958821 DOI: 10.1038/s41467-025-58377-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 03/20/2025] [Indexed: 04/02/2025] Open
Abstract
Skin microecology involves a dynamic equilibrium among the host, microbiome, and internal/external environments. This equilibrium, shaped by multifactorial interactions, reflects individual specificity and diversity. Creating a replicable in vitro skin microecological model is highly challenging. Here, we introduce a mimicked stratum corneum microecology model (SCmic). It uses light cured crosslinked hydrogels as a scaffold and moisture source, and nonviable epidermal cells as the main nutrient. This setup establishes a suitable, stable, and reproducible microecology for microbiome colonization. Notably, it replicates the normal/oily skin microbiota with no significant differences from the original native microbiota at the genus level. Simultaneously, we have developed a standardized human skin microbiota model (Hcm), featuring seven dominant strains that form a representative microbial community. The models provide highly convenient approaches for exploring the intricate mutual interactions among skin microecology, influence of microbiota on skin health, and metabolism of chemical substances by microbiota.
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Affiliation(s)
- Pan Wang
- Skin Health and Cosmetic Development & Evaluation Laboratory, China Pharmaceutical University, Nanjing, 211198, Jiangsu, China
| | - Huijuan Li
- Skin Health and Cosmetic Development & Evaluation Laboratory, China Pharmaceutical University, Nanjing, 211198, Jiangsu, China
| | - Xingjiang Zhang
- Skin Health and Cosmetic Development & Evaluation Laboratory, China Pharmaceutical University, Nanjing, 211198, Jiangsu, China
| | - Xiaoxun Wang
- Skin Health and Cosmetic Development & Evaluation Laboratory, China Pharmaceutical University, Nanjing, 211198, Jiangsu, China
| | - Wenwen Sun
- Skin Health and Cosmetic Development & Evaluation Laboratory, China Pharmaceutical University, Nanjing, 211198, Jiangsu, China
| | - Xiaoya Zhang
- Skin Health and Cosmetic Development & Evaluation Laboratory, China Pharmaceutical University, Nanjing, 211198, Jiangsu, China
| | - Baiyi Chi
- Skin Health and Cosmetic Development & Evaluation Laboratory, China Pharmaceutical University, Nanjing, 211198, Jiangsu, China
| | - Yuyo Go
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Xi Hui Felicia Chan
- Department of Medicine, Waikato hospital, 183 Pembroke Street, Hamilton, 3204, New Zealand
| | - Jianxin Wu
- Skin Health and Cosmetic Development & Evaluation Laboratory, China Pharmaceutical University, Nanjing, 211198, Jiangsu, China.
| | - Qing Huang
- Skin Health and Cosmetic Development & Evaluation Laboratory, China Pharmaceutical University, Nanjing, 211198, Jiangsu, China.
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Lee TY, Liao YC, Chang HT, Lin HC, Weng HM, Chang IJ, Young SL, Shen PC, Bhattarai BP, Lin JS, Lee JW. Inclusion of Multi-Strained Probiotics Improves the Fecal Microbiota and Carcass Quality of Pigs. Animals (Basel) 2025; 15:993. [PMID: 40218386 PMCID: PMC11987732 DOI: 10.3390/ani15070993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2025] [Revised: 03/25/2025] [Accepted: 03/28/2025] [Indexed: 04/14/2025] Open
Abstract
Limited studies have addressed the effects of multi-strain probiotics on gut microbiota and their influence on meat traits in pigs. Thus, this study investigated the impact of including a commercialized multi-strain probiotic product (SYN) (SYNLAC-LeanAd) into the dietary regimen of crossbred Landrace × Yorkshire × Duroc (LYD) pigs. The study spanned a duration of 22 weeks, from weaning until slaughtering, during which the carcass traits, meat quality, and fecal microbiota profile were compared to those of pigs fed diets with or without an antibiotic growth promoter (AGP). The results demonstrated that the inclusion of SYN significantly improved meat quality parameters, including marbling score, tenderness, and intramuscular fat (p < 0.05) in comparison to pigs fed with AGP. The analysis of fecal microbiota revealed that SYN inclusion increased the populations of Clostridiaceae, Coriobacteriaceae, and Erysipelotrichaceae compared to the control and AGP groups. Additionally, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis predicted that the amino acid and lipid metabolism pathways were facilitated in pigs from the SYN group. These findings suggest that the inclusion of SYNLAC-LeanAd has the potential to positively impact the fecal microbiota profile, which in turn may lead to improved carcass traits and meat quality in commercial crossbred pigs.
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Affiliation(s)
- Ting-Yu Lee
- Synbio Tech Inc., Kaohsiung 821011, Taiwan; (T.-Y.L.); (Y.-C.L.); (H.-T.C.); (H.-C.L.); (H.-M.W.); (I.-J.C.); (S.-L.Y.)
| | - Yi-Chu Liao
- Synbio Tech Inc., Kaohsiung 821011, Taiwan; (T.-Y.L.); (Y.-C.L.); (H.-T.C.); (H.-C.L.); (H.-M.W.); (I.-J.C.); (S.-L.Y.)
| | - Hsiao-Tung Chang
- Synbio Tech Inc., Kaohsiung 821011, Taiwan; (T.-Y.L.); (Y.-C.L.); (H.-T.C.); (H.-C.L.); (H.-M.W.); (I.-J.C.); (S.-L.Y.)
| | - Hsiao-Ching Lin
- Synbio Tech Inc., Kaohsiung 821011, Taiwan; (T.-Y.L.); (Y.-C.L.); (H.-T.C.); (H.-C.L.); (H.-M.W.); (I.-J.C.); (S.-L.Y.)
| | - Hsiu-Ming Weng
- Synbio Tech Inc., Kaohsiung 821011, Taiwan; (T.-Y.L.); (Y.-C.L.); (H.-T.C.); (H.-C.L.); (H.-M.W.); (I.-J.C.); (S.-L.Y.)
| | - I-Ju Chang
- Synbio Tech Inc., Kaohsiung 821011, Taiwan; (T.-Y.L.); (Y.-C.L.); (H.-T.C.); (H.-C.L.); (H.-M.W.); (I.-J.C.); (S.-L.Y.)
| | - San-Land Young
- Synbio Tech Inc., Kaohsiung 821011, Taiwan; (T.-Y.L.); (Y.-C.L.); (H.-T.C.); (H.-C.L.); (H.-M.W.); (I.-J.C.); (S.-L.Y.)
| | - Perng-Chih Shen
- Department of Animal Science, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan;
| | - Bishnu Prasad Bhattarai
- Department of Tropical Agriculture and International Cooperation, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan;
| | - Jin-Seng Lin
- Synbio Tech Inc., Kaohsiung 821011, Taiwan; (T.-Y.L.); (Y.-C.L.); (H.-T.C.); (H.-C.L.); (H.-M.W.); (I.-J.C.); (S.-L.Y.)
| | - Jai-Wei Lee
- Department of Tropical Agriculture and International Cooperation, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan;
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143
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Li S, Peng Y, Li M, Li X, Li H, Dabu X, Yang Y. Different active exogenous carbons improve the yield and quality of roses by shaping different bacterial communities. Front Microbiol 2025; 16:1558322. [PMID: 40226102 PMCID: PMC11985833 DOI: 10.3389/fmicb.2025.1558322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2025] [Accepted: 03/14/2025] [Indexed: 04/15/2025] Open
Abstract
The application of exogenous organic carbon represents a significant strategy for enhancing soil fertility and promoting sustainable agricultural development. This approach modifies the physicochemical properties of soil and influences microbial community structures, consequently improving crop yield and quality. Nevertheless, the mechanisms underlying microbial community responses to various forms of active exogenous organic carbon remain poorly understood and require further investigation. A 1-year follow-up experiment was conducted to examine the effects of different carbon sources on the yield and quality of cut roses, along with the characteristics of the soil bacterial community. The results indicated that applying organic fertiliser and biochar significantly enhanced the productivity of cut roses, demonstrating a sustained growth-promoting effect. Organic fertiliser provides more active, readily oxidisable organic carbon to the soil compared to biochar. In contrast, biochar supplies stable organic carbon, including inert organic carbon that is difficult to oxidise, firm organic carbon (FOC), and total inert organic carbon, which has a high degree of humification that significantly exceeds that of organic fertiliser. The application of biochar and organic fertiliser not only altered the abundance, diversity, and composition of the rhizosphere microbial community but also enriched beneficial microorganisms. Redundancy analysis results indicated that FOC, available phosphorus, and soil organic matter were the primary factors influencing the bacterial community. The results of this study demonstrated that exogenous organic carbon exerted positive and indirect effects on crop yield by influencing soil properties and bacterial communities. These findings provide novel evidence supporting the rational application of biochar and organic fertilisers as a means to promote agricultural sustainability in red soil regions.
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Affiliation(s)
- Shixiong Li
- College of Resources and Environment, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Yuanyang Peng
- College of Resources and Environment, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Manying Li
- College of Resources and Environment, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Xin Li
- College of Resources and Environment, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Haoyang Li
- College of Resources and Environment, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Xilatu Dabu
- College of Resources and Environment, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Yun Yang
- Yunnan Huayan Agricultural Science and Technology Co., Ltd., Kunming, China
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Nieciecki VF, Blum FC, Johnson RC, Testerman TL, McAvoy TJ, King MC, Gushchin V, Whitmire JM, Frey KG, Glang L, Peña-Gomez D, Bishop-Lilly KA, Sardi A, Merrell DS, Metcalf JL. Cross-laboratory replication of pseudomyxoma peritonei tumor microbiome reveals reproducible microbial signatures. mSphere 2025; 10:e0065224. [PMID: 39976448 PMCID: PMC11934312 DOI: 10.1128/msphere.00652-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Accepted: 01/21/2025] [Indexed: 02/21/2025] Open
Abstract
Recent work has demonstrated that cancer-specific microbial communities often colonize tumor tissues. However, untangling low-biomass signals from environmental contamination makes this research technically challenging. We utilize pseudomyxoma peritonei (PMP), a cancer characterized by the spread of mucus-secreting cells throughout the peritoneal cavity, to develop a robust workflow for identifying reproducible tumor microbiomes. Typically originating from the rupture of an appendiceal tumor into the peritoneal cavity, metastasized tumors have been previously shown to harbor a core set of microbes. However, that work did not control for the potential contamination of these low microbial biomass samples. We expand upon these prior findings by characterizing the microbiome of 70 additional PMP tumors and six normal peritoneal control tissues along with appropriate laboratory controls. Additionally, DNA from a subset of 25 tissues was extracted and sequenced at an independent laboratory. We found evidence of reproducible microbial signatures between the replicates of six different PMP tumors that include a set of core taxa that may be introduced from surgical contamination, as well as patient-specific taxa that are also commonly implicated in colorectal cancer. In addition, preoperative chemotherapy treatment was found to reduce tumor microbiome diversity. Our findings demonstrate how independent sample replication can be a powerful approach to investigate low-biomass microbial communities associated with tumor tissues that will improve low microbial biomass research.IMPORTANCERecent work has demonstrated that microbial communities colonize over 30 different types of tumor tissues. The origin of these communities and their possible involvement in carcinogenesis or cancer treatment outcomes remains an unclear, yet important area of research. A current major challenge in characterizing low-biomass, tumor-associated microbiomes is the introduction of environmental contamination during collection, handling, DNA extraction, PCR, and sequencing. Here, we provide a framework for replicating low-biomass tumor microbiome samples to help identify tumors with robust microbial signals and low background contamination. Using this replication approach, we show that pseudomyxoma peritonei (PMP) tumors host reproducible microbial communities, including organisms that have previously been associated with colorectal cancer. Incorporating sample replication into future tumor microbiome studies is a promising approach that will help identify robust signals and increase reproducibility in the field.
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Affiliation(s)
- Victoria F. Nieciecki
- Graduate Program in Cell & Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Faith C. Blum
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, Maryland, USA
| | | | - Traci L. Testerman
- School of Medicine, University of South Carolina, Columbia, South Carolina, USA
| | - Tom J. McAvoy
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland, USA
| | - Mary Caitlin King
- Department of Surgical Oncology, The Institute for Cancer Care at Mercy, Mercy Medical Center, Baltimore, Maryland, USA
| | - Vadim Gushchin
- Department of Surgical Oncology, The Institute for Cancer Care at Mercy, Mercy Medical Center, Baltimore, Maryland, USA
| | - Jeannette M. Whitmire
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, Maryland, USA
| | - Kenneth G. Frey
- Genomics & Bioinformatics Department, Naval Medical Research Command, NMRC-Frederick, Fort Detrick, Maryland, USA
| | - Lindsay Glang
- Genomics & Bioinformatics Department, Naval Medical Research Command, NMRC-Frederick, Fort Detrick, Maryland, USA
- Leidos, Reston, Virginia, USA
| | - Dessiree Peña-Gomez
- Genomics & Bioinformatics Department, Naval Medical Research Command, NMRC-Frederick, Fort Detrick, Maryland, USA
- Leidos, Reston, Virginia, USA
| | - Kimberly A. Bishop-Lilly
- Genomics & Bioinformatics Department, Naval Medical Research Command, NMRC-Frederick, Fort Detrick, Maryland, USA
| | - Armando Sardi
- Department of Surgical Oncology, The Institute for Cancer Care at Mercy, Mercy Medical Center, Baltimore, Maryland, USA
| | - D. Scott Merrell
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, Maryland, USA
| | - Jessica L. Metcalf
- Graduate Program in Cell & Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA
- Canadian Institute for Advanced Research Global Scholar, Toronto, Ontario, Canada
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145
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Khan MM, Mushtaq MA, Suleman M, Ahmed U, Ashraf MF, Aslam R, Mohsin M, Rödiger S, Sarwar Y, Schierack P, Ali A. Fecal microbiota landscape of commercial poultry farms in Faisalabad, Pakistan: A 16S rRNA gene-based metagenomics study. Poult Sci 2025; 104:105089. [PMID: 40187012 PMCID: PMC12002918 DOI: 10.1016/j.psj.2025.105089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2025] [Revised: 03/21/2025] [Accepted: 03/21/2025] [Indexed: 04/07/2025] Open
Abstract
This study explores the microbiota of broiler and layer farms, aiming to understand how genetic breed, age, and farm type influence microbial communities in commercial settings. Fecal samples from 18 poultry farms (twelve layers and six broilers) in Faisalabad, Pakistan were analyzed using 16S rRNA gene sequencing of the V3-V4 region to evaluate bacterial composition. The dominant phylum, Firmicutes, accounted for 58.72 % of the microbial population, with Lactobacillus being the most abundant genus in both broilers and layers. The total abundance of potentially pathogenic genera was also assessed with Enterococcus and Corynebacterium being the most prevalent across all farms, regardless of bird type. Layers exhibited greater microbial richness and diversity than broilers, while the Karachi cage system (KCS) farm type showed higher richness than Floor system (FS). Although the breed significantly influenced microbial diversity, age was not a determining factor. Co-occurrence analyses revealed close interactions among phyla (Actinobacteriota, Proteobacteria, Firmicutes, Fusobacteriota, and Bacteroidota) and genera (Lactobacillus, Brevibacterium, Enterococcus), suggesting their pivotal roles within the microbial community. Additionally, functional analysis detected important metabolic pathways and traced microbial signatures of key pathogenic bacteria, enhancing our understanding of microbial contributions to poultry health. Despite limitations such as the need for broader geographic sampling and accounting for diet and medication, this study advances microbiome research in Pakistan's poultry sector, emphasizing consistent taxa and opening avenues for future investigations into microbiome manipulations for improved food safety and achieve better sustainable practices.
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Affiliation(s)
- Muhammad Moman Khan
- Institute for Biotechnology, Brandenburg University of Technology (BTU) Cottbus-Senftenberg, Senftenberg, Germany
| | - Muhammad Ahmed Mushtaq
- Institute for Biotechnology, Brandenburg University of Technology (BTU) Cottbus-Senftenberg, Senftenberg, Germany
| | | | - Umer Ahmed
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Faisal Ashraf
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Rizwan Aslam
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan
| | - Mashkoor Mohsin
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan
| | - Stefan Rödiger
- Institute for Biotechnology, Brandenburg University of Technology (BTU) Cottbus-Senftenberg, Senftenberg, Germany
| | - Yasra Sarwar
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Peter Schierack
- Institute for Biotechnology, Brandenburg University of Technology (BTU) Cottbus-Senftenberg, Senftenberg, Germany
| | - Aamir Ali
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan.
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146
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Wong MK, Boukhaled GM, Armstrong E, Liu R, Heirali AA, Yee NR, Tsang J, Spiliopoulou P, Schneeberger PHH, Wang BX, Cochrane K, Sherriff K, Allen-Vercoe E, Siu LL, Spreafico A, Coburn B. Microbial Ecosystem Therapeutics 4 (MET4) elicits treatment-specific IgG responses associated with changes in gut microbiota in immune checkpoint inhibitor recipients with advanced solid tumors. J Immunother Cancer 2025; 13:e010681. [PMID: 40121033 PMCID: PMC11979602 DOI: 10.1136/jitc-2024-010681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2024] [Accepted: 03/06/2025] [Indexed: 03/25/2025] Open
Abstract
BACKGROUND Gut microbiome modulation has shown promise in its potential to treat cancer in combination with immunotherapy. Mechanistically, the pathways and routes by which gut microbiota may influence systemic and antitumor immunity remain uncertain. Here, we used blood and stool samples from Microbial Ecosystem Therapeutic 4 (MET4)-IO, an early-phase trial testing the safety and engraftment of the MET4 bacterial consortium in immune checkpoint inhibitor recipients, to assess how MET4 may affect systemic immunity. METHODS Circulating antibody responses induced by MET4 were assessed using an antimicrobial antibody flow cytometry assay on pretreatment and post-treatment plasma. Antibody responses were associated with taxonomic changes in stool identified by metagenomic sequencing. Mass cytometry was performed on peripheral blood mononuclear cells to identify shifts in circulating immune subsets associated with antibody responses. RESULTS Increases in circulating anti-MET4 immunoglobulin G (IgG) responses were measured by flow cytometry post-consortium treatment in MET4 recipients, but not untreated control participants, with five individuals displaying notably higher antibody responses. Stronger IgG responses were associated with greater increases in multiple taxa, including MET4 microbe Collinsella aerofaciens, which was previously linked with immune checkpoint response. However, these taxa were not enriched in the IgG-bound fraction post-MET4 treatment. Greater increases in circulating B cells and FoxP3+ CD4+ T cells post-MET4 treatment were observed in the blood of high IgG responders, while CD14+ and CD16+ monocyte populations were decreased in these individuals. CONCLUSION These results demonstrate the induction of treatment-specific circulating humoral immunity by a bacterial consortium and suggest potential mechanisms by which gut microbes may contribute to antitumor immunity.
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Affiliation(s)
- Matthew K Wong
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Giselle M Boukhaled
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Eric Armstrong
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Rachel Liu
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Alya A Heirali
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Noelle R Yee
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Jinny Tsang
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Pavlina Spiliopoulou
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Pierre H H Schneeberger
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Ben X Wang
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | | | | | | | - Lillian L Siu
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Anna Spreafico
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Bryan Coburn
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
- Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, Ontario, Canada
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147
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Delicati A, Marcante B, Catelan D, Biggeri A, Caenazzo L, Tozzo P. Hand-to-surface bacterial transfer and healthcare-associated infections prevention: a pilot study on skin microbiome in a molecular biology laboratory. Front Med (Lausanne) 2025; 12:1546298. [PMID: 40190580 PMCID: PMC11970135 DOI: 10.3389/fmed.2025.1546298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2024] [Accepted: 03/06/2025] [Indexed: 04/09/2025] Open
Abstract
Background Healthcare-associated infections (HAIs) are a major global public health problem, contributing significantly to patient morbidity and mortality. This study analyses differences in type and amounts of bacteria transferred from volunteers' dominant palm to two healthcare-relevant surfaces (glass and laminate table), both before and after hand washing with water and antibacterial soap. The aim was to understand hand-to-surface microbial contamination and support the development of HAI prevention strategies. Methods Microbial DNA was extracted and sequenced to identify bacteria species. Taxonomic and statistical analyses were performed to evaluate bacterial diversity and abundance across the experimental groups. Results The results confirmed greater bacteria abundance and species richness on palm compared to surfaces, with a significant reduction after hand washing, especially on glass. Taxa analysis highlighted the increased persistence of Gram-negative HAIs-related bacteria on laminate surface, while Gram-positive opportunistic bacteria were more abundant on palms and glass surface. Beta diversity confirmed significant differences in microbial composition between the groups, highlighting the importance of bacteria-surface characteristics in designing preventive measures. Conclusion Despite some limitations, our study emphasizes the importance of microbiological surveillance for all opportunistic bacteria with pathogenic potential. These findings can contribute to more effective guidelines for surface disinfection and hand washing, key elements in preventing HAIs.
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Affiliation(s)
- Arianna Delicati
- Legal Medicine Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Padova, Italy
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
- Unit of Biostatistics, Epidemiology and Public Health, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Padova, Italy
| | - Beatrice Marcante
- Legal Medicine Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Padova, Italy
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
- Unit of Biostatistics, Epidemiology and Public Health, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Padova, Italy
| | - Dolores Catelan
- Unit of Biostatistics, Epidemiology and Public Health, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Padova, Italy
| | - Annibale Biggeri
- Unit of Biostatistics, Epidemiology and Public Health, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Padova, Italy
| | - Luciana Caenazzo
- Legal Medicine Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Padova, Italy
| | - Pamela Tozzo
- Legal Medicine Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Padova, Italy
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148
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Zhang Z, Li Y, Zhang D, Chen S, Lu S, Wang K, Zhou M, Song Z, Li Q, Yin J, Liu X. FACdb: a comprehensive resource for genes, gut microbiota, and metabolites in farm animals. Front Microbiol 2025; 16:1557285. [PMID: 40190740 PMCID: PMC11968756 DOI: 10.3389/fmicb.2025.1557285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2025] [Accepted: 02/28/2025] [Indexed: 04/09/2025] Open
Abstract
Farm animals, including livestock and poultry, play essential economic, social, and cultural roles and are indispensable in human welfare. Farm Animal Connectome database (FACdb) is a comprehensive resource that includes the association networks among gene expression, gut microbiota, and metabolites in farm animals. Although some databases present the relationship between gut microbes, metabolites, and gene expression, these databases are limited to human and mouse species, with limited data for farm animals. In this database, we calculate the associations and summarize the connections among gene expression, gut microbiota, and metabolites in farm animals using six correlation or distance calculation (including Pearson, Spearman, Cosine, Euclidean, Bray-Curtis, and Mahalanobis). FACdb contains over 55 million potential interactions of 73,571 genes, 11,046 gut microbiota, and 4,540 metabolites. It provides an easy-to-use interface for browsing and searching the association information. Additionally, FACdb offers interactive visualization tools to effectively investigate the relationship among the genes, gut microbiota, and metabolites in farm animals. Overall, FACdb is a valuable resource for understanding interactions among gut microbiota, metabolites, and gene expression. It contributes to the further utilization of microbes in animal products and welfare promotion. Compared to mice, pigs or other farm animals share more similarities with humans in molecular, cellular, and organ-level responses, indicating that our database may offer new insights into the relationship among gut microbiota, metabolites, and gene expression in humans.
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Affiliation(s)
- Ze Zhang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
- BGI Research, Hangzhou, China
| | - Yang Li
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Di Zhang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Shuai Chen
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Sien Lu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Kang Wang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Miao Zhou
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Zehe Song
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Qingcui Li
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Jie Yin
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Xiaoping Liu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
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149
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Cano-Argüelles AL, Wu-Chuang A, Mateos-Hernandez L, Abuin-Denis L, Maitre A, Avellanet J, García A, Fuentes D, Cabezas-Cruz A. Protocol to study the impact of breast cancer on colonization resistance of mouse microbiota using network node manipulation. STAR Protoc 2025; 6:103618. [PMID: 39921860 PMCID: PMC11851282 DOI: 10.1016/j.xpro.2025.103618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2024] [Revised: 11/24/2024] [Accepted: 01/13/2025] [Indexed: 02/10/2025] Open
Abstract
Network analysis is a powerful tool for investigating complex interactions between different microbial taxa within a community. We present a protocol to study the gut microbial community in a mouse model of breast cancer using a network-based approach. Here, we describe the procedures for tumor cell production and inoculation and 16S rRNA data processing. We then detail steps for constructing co-occurrence networks based on correlations between microbial abundances. For complete details on the use and execution of this protocol, please refer to Wu-Chuang et al.1.
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Affiliation(s)
- Ana Laura Cano-Argüelles
- Parasitology Laboratory, Institute of Natural Resources and Agrobiology of Salamanca (IRNASA, CSIC), Cordel de Merinas, 40-52, 37008 Salamanca, Spain
| | - Alejandra Wu-Chuang
- Anses, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, 94700 Maisons-Alfort, France.
| | - Lourdes Mateos-Hernandez
- Anses, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, 94700 Maisons-Alfort, France
| | - Lianet Abuin-Denis
- Anses, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, 94700 Maisons-Alfort, France; Animal Biotechnology Department, Center for Genetic Engineering and Biotechnology, Avenue 31 between 158 and 190, P.O. Box 6162, Havana 10600, Cuba
| | - Apolline Maitre
- Anses, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, 94700 Maisons-Alfort, France; INRAE, UR 0045 Laboratoire de Recherches Sur Le Développement de L'Elevage (SELMET-LRDE), Corte, France; EA 7310, Laboratoire de Virologie, Université de Corse, Corte, France
| | - Janet Avellanet
- Center of Molecular Immunology (CIM), Calle 15 esq. 216, Atabey, Playa, Havana, Cuba
| | - Arlem García
- Center of Molecular Immunology (CIM), Calle 15 esq. 216, Atabey, Playa, Havana, Cuba
| | - Dasha Fuentes
- National Center for Laboratory Animal Breeding (CENPALAB), Calle 3ra # 40759 entre 6ta y carretera de Tirabeque, Rpto La Unión, Boyeros, Havana, Cuba.
| | - Alejandro Cabezas-Cruz
- Anses, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, 94700 Maisons-Alfort, France.
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Ko MJ, Liao CH, Chiu YL, Tsai WC, Yang JY, Pai MF, Tsai PH, Hsu SP, Peng YS, Wu HY. Gut microbial signatures associated with uremic pruritus in hemodialysis patients. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2025:S1684-1182(25)00072-6. [PMID: 40155303 DOI: 10.1016/j.jmii.2025.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2024] [Revised: 02/09/2025] [Accepted: 03/15/2025] [Indexed: 04/01/2025]
Abstract
BACKGROUND The gut microbiota influences the gut-skin-kidney axis, but its role in uremic pruritus remains poorly understood. This study aimed to explore differences in gut microbial profiles between hemodialysis (HD) patients with and without uremic pruritus and identify potential microbial signatures associated with uremic pruritus. METHODS We conducted a cross-sectional study of HD patients with and without uremic pruritus. Stool samples were collected from all participants, and the gut microbiota composition was analyzed using 16S rRNA gene sequencing. Alpha and beta diversity metrics were calculated to assess microbial diversity. LEfSe analysis was performed to identify differentially abundant taxa associated with uremic pruritus. RESULTS Among 93 HD patients (mean age: 61.9 years, 31.2 % female), uremic pruritus occurred in 61.3 % of patients, with a median visual analog scale (VAS) score of 4.0. While alpha diversity did not differ significantly between groups, beta diversity analysis revealed significant compositional differences (unweighted UniFrac metric, P = 0.004; weighted UniFrac metric, P < 0.001). LEfSe analysis revealed significant enrichment of the order Pasteurellales, family Pasteurellaceae and genus Dialister in patients with uremic pruritus, whereas the order Corynebacteriales was more abundant in patients without pruritus (P < 0.05, LDA score > 3). CONCLUSION In this study, we found significant differences in gut microbiota composition between HD patients with and without uremic pruritus and identified potential microbial biomarkers for uremic pruritus. Further studies are needed to elucidate the underlying mechanisms and explore microbiota-targeted therapeutic interventions.
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Affiliation(s)
- Mei-Ju Ko
- Department of Dermatology, Taipei City Hospital, Taipei City, Taiwan; Department of Dermatology, National Taiwan University Hospital and College of Medicine, Taipei City, Taiwan; School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei City, Taiwan; University of Taipei, Taipei City, Taiwan
| | - Chun-Hsing Liao
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei City, Taiwan; Department of Internal Medicine, Far Eastern Memorial Hospital, New Taipei City, Taiwan
| | - Yen-Ling Chiu
- Department of Internal Medicine, Far Eastern Memorial Hospital, New Taipei City, Taiwan; Department of Medical Research, Far Eastern Memorial Hospital, New Taipei City, Taiwan; Graduate Program in Biomedical Informatics, Yuan Ze University, Taoyuan City, Taiwan; Graduate Institute of Medicine, Yuan Ze University, Taoyuan City, Taiwan
| | - Wan-Chuan Tsai
- Department of Internal Medicine, Far Eastern Memorial Hospital, New Taipei City, Taiwan; Center for General Education, Lee-Ming Institute of Technology, New Taipei City, Taiwan
| | - Ju-Yeh Yang
- Department of Internal Medicine, Far Eastern Memorial Hospital, New Taipei City, Taiwan; Center for General Education, Lee-Ming Institute of Technology, New Taipei City, Taiwan
| | - Mei-Fen Pai
- Department of Internal Medicine, Far Eastern Memorial Hospital, New Taipei City, Taiwan
| | - Ping-Hsiu Tsai
- Department of Internal Medicine, Far Eastern Memorial Hospital, New Taipei City, Taiwan
| | - Shih-Ping Hsu
- Department of Internal Medicine, Far Eastern Memorial Hospital, New Taipei City, Taiwan; School of Life Science, National Taiwan Normal University, Taipei City, Taiwan
| | - Yu-Sen Peng
- Department of Internal Medicine, Far Eastern Memorial Hospital, New Taipei City, Taiwan; Department of Applied Cosmetology, Lee-Ming Institute of Technology, New Taipei City, Taiwan; Department of Healthcare Administration, Asia Eastern University of Science and Technology, New Taipei City, Taiwan
| | - Hon-Yen Wu
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei City, Taiwan; Department of Internal Medicine, Far Eastern Memorial Hospital, New Taipei City, Taiwan; Department of Medical Research, Far Eastern Memorial Hospital, New Taipei City, Taiwan; Department of Internal Medicine, National Taiwan University Hospital and College of Medicine, Taipei City, Taiwan; Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei City, Taiwan.
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