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Kumar R, Gandham S, Bhaskar V, Praharaj MR, Maity HK, Sarkar U, Dey B. Transcriptomic insights into Mycobacterium orygis infection-associated pulmonary granulomas reveal multicellular immune networks and tuberculosis biomarkers in cattle. Vet Q 2025; 45:1-19. [PMID: 40432328 PMCID: PMC12120866 DOI: 10.1080/01652176.2025.2509503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2024] [Revised: 04/11/2025] [Accepted: 05/17/2025] [Indexed: 05/29/2025] Open
Abstract
Mycobacterium orygis, a member of the Mycobacterium tuberculosis complex (MTBC), has emerged as a significant contributor to tuberculosis (TB) in cattle, wildlife, and humans. However, understanding about its pathogenesis and severity is limited, compounded by the lack of reliable TB biomarkers in cattle. This study delves into the comparative pathology and transcriptomic landscape of pulmonary granulomas in cattle naturally infected with M. orygis, using high-throughput RNA sequencing. Histopathological analysis revealed extensive, multistage granulomatous, necrotic, and cavitary lesions, indicative of severe lung pathology induced by M. orygis. Transcriptomic profiling highlighted numerous differentially expressed genes and dysregulated pathways related to immune response modulation and extracellular matrix remodelling. Additionally, cell type enrichment analysis provided insights into the multicellularity of the granulomatous niche, emphasising complex cell-cell interactions within TB granulomas. Via comparative transcriptomics leveraging publicly available bovine and human TB omics datasets, 14 key immunomodulators (SOD2, IL1α/β, IL15, IL18, CCL2/MCP-1, CCL3/MIP-1α, CCL4/MIP-1β, CCL8/MCP-2, CCL20/MIP-3α, CXCL2/MIP-2, CXCL10/IP-10, CXCL11, and IFN-γ) were identified as potential biomarkers for active TB in cattle. These findings significantly advance our understanding of M. orygis pathogenesis in bovine TB and highlight potential targets for the development of diagnostic tools for managing and controlling the disease.
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Affiliation(s)
- Rishi Kumar
- National Institute of Animal Biotechnology, Hyderabad, Telangana, India
- Regional Centre for Biotechnology, Faridabad, Haryana, India
| | - Sripratyusha Gandham
- National Institute of Animal Biotechnology, Hyderabad, Telangana, India
- Regional Centre for Biotechnology, Faridabad, Haryana, India
| | - Vinay Bhaskar
- National Institute of Animal Biotechnology, Hyderabad, Telangana, India
| | - Manas Ranjan Praharaj
- National Institute of Animal Biotechnology, Hyderabad, Telangana, India
- Regional Centre for Biotechnology, Faridabad, Haryana, India
| | - Hemanta Kumar Maity
- Department of Avian Sciences, West Bengal University of Animal and Fishery Sciences, Kolkata, West Bengal, India
| | - Uttam Sarkar
- Department of Animal Genetics and Breeding, West Bengal University of Animal and Fishery Sciences, Kolkata, West Bengal, India
| | - Bappaditya Dey
- National Institute of Animal Biotechnology, Hyderabad, Telangana, India
- Regional Centre for Biotechnology, Faridabad, Haryana, India
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2
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Dong X, Xiang Y, Li L, Zhang Y, Wu T. Genomic insights into the rapid rise of Pseudomonas aeruginosa ST463: A high-risk lineage's adaptive strategy in China. Virulence 2025; 16:2497901. [PMID: 40320374 PMCID: PMC12051580 DOI: 10.1080/21505594.2025.2497901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2024] [Revised: 12/19/2024] [Accepted: 04/17/2025] [Indexed: 05/08/2025] Open
Abstract
High-risk lineages of Pseudomonas aeruginosa pose a serious threat to public health, causing severe infections with high mortality rates and limited treatment options. The emergence and rapid spread of the high-risk lineage ST463 in China have further exacerbated this issue. However, the basis of its success in China remains unidentified. In this study, we analyzed a comprehensive dataset of ST463 strains from 2000 to 2023 using whole genome sequencing to unravel the epidemiological characteristics, evolutionary trajectory, and antibiotic resistance profiles. Our findings suggest that ST463 likely originated from a single introduction from North America in 2007, followed by widespread domestic dissemination. Since its introduction, the lineage has undergone significant genomic changes, including the acquisition of three unique regions that enhanced its metabolism and adaptability. Frequent recombination events, along with the burden of bacteriophages, antibiotic resistance genes, and the spread of c1-type (blaKPC-2) plasmid-carrying strains, have played crucial roles in its expansion in China. Mutation analysis reveals adaptive responses to antibiotics and selective pressures on key virulence factors, indicating that ST463 is evolving toward a more pathogenic lifestyle.
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Affiliation(s)
- Xu Dong
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yanghui Xiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ying Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| | - Tiantian Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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3
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Ryt-Hansen P, George S, Hjulsager CK, Trebbien R, Krog JS, Ciucani MM, Langerhuus SN, DeBeauchamp J, Crumpton JC, Hibler T, Webby RJ, Larsen LE. Rapid surge of reassortant A(H1N1) influenza viruses in Danish swine and their zoonotic potential. Emerg Microbes Infect 2025; 14:2466686. [PMID: 39945729 PMCID: PMC11849018 DOI: 10.1080/22221751.2025.2466686] [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: 12/03/2024] [Revised: 02/05/2025] [Accepted: 02/07/2025] [Indexed: 02/22/2025]
Abstract
In 2018, a single detection of a novel reassortant swine influenza A virus (swIAV) was made in Denmark. The hemagglutinin (HA) of the virus was from the H1N1 pandemic 2009 (H1N1pdm09) lineage and the neuraminidase (NA) from the H1N1 Eurasian avian-like swine lineage (H1N1av). By 2022, the novel reassortant virus (H1pdm09N1av) constituted 27% of swIAVs identified through the Danish passive swIAV surveillance program. Sequencing detected two H1pdm09N1av genotypes; Genotype 1 contained an entire internal gene cassette of H1N1pdm09 origin, Genotype 2 differed by carrying an NS gene segment of H1N1av origin. The internal gene cassette of Genotype 2 became increasingly dominant, not only in the H1pdm09N1av population, but also in other Danish enzootic swIAV subtypes. Phylogenetic analysis of the HA genes from H1pdm09N1av viruses revealed a monophyletic source, a higher substitution rate compared to other H1N1pdm09 viruses and genetic differences with human seasonal and other swine adapted H1N1pdm09 viruses. Correspondingly, H1pdm09N1av viruses were antigenically distinct from human H1N1pdm09 vaccine viruses. Both H1pdm09N1av genotypes transmitted between ferrets by direct contact, but only Genotype 1 was capable of efficient aerosol transmission. The rapid spread of H1pdm09N1av viruses in Danish swine herds is concerning for swine and human health. Their zoonotic threat is highlighted by the limited pre-existing immunity observed in the human population, aerosol transmission in ferrets and the finding that the internal gene cassette of Genotype 2 was present in the first two zoonotic influenza infections ever detected in Denmark.
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Affiliation(s)
- Pia Ryt-Hansen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Sophie George
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | | | - Ramona Trebbien
- Department for Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen S, Denmark
| | - Jesper Schak Krog
- Department for Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen S, Denmark
| | - Marta Maria Ciucani
- Department for Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen S, Denmark
| | | | - Jennifer DeBeauchamp
- Department of Host-Microbe Interactions, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Jeri Carol Crumpton
- Department of Host-Microbe Interactions, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Taylor Hibler
- Department of Host-Microbe Interactions, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Richard J. Webby
- Department of Host-Microbe Interactions, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Lars Erik Larsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
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4
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Jiao Y, Ren J, Xie S, Yuan N, Shen J, Yin H, Wang J, Guo H, Cao J, Wang X, Wu D, Zhou Z, Qi X. Raffinose-metabolizing bacteria impair radiation-associated hematopoietic recovery via the bile acid/FXR/NF-κB signaling pathway. Gut Microbes 2025; 17:2488105. [PMID: 40192235 PMCID: PMC11980471 DOI: 10.1080/19490976.2025.2488105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2024] [Revised: 03/23/2025] [Accepted: 03/28/2025] [Indexed: 04/11/2025] Open
Abstract
Radiation-associated hematopoietic recovery (RAHR) is critical for mitigating lethal complications of acute radiation syndrome (ARS), yet therapeutic strategies remain limited. Through integrated multi-omics analysis of a total body irradiation (TBI) mouse model, we identify Bacteroides acidifaciens-dominated gut microbiota as key mediators of RAHR impairment. 16S ribosomal rRNA sequencing revealed TBI-induced dysbiosis characterized by Bacteroidaceae enrichment, while functional metagenomics identified raffinose metabolism as the most significantly perturbed pathway. Notably, raffinose supplementation (10% w/v) recapitulated radiation-induced microbiota shifts and delayed bone marrow recovery. Fecal microbiota transplantation (FMT) revealed a causative role for raffinose-metabolizing microbiota, particularly Bacteroides acidifaciens, in delaying RAHR progression. Mechanistically, B. acidifaciens-mediated bile acid deconjugation activated FXR, subsequently suppressing NF-κB-dependent hematopoietic recovery. Therapeutic FXR inhibition via ursodeoxycholic acid (UDCA) had been shown to be a viable method for rescuing RAHR. Our results delineated a microbiome-bile acid-FXR axis as a master regulator of post-irradiation hematopoiesis. Targeting B. acidifaciens or its metabolic derivatives could represent a translatable strategy to mitigate radiation-induced hematopoietic injury.
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Affiliation(s)
- Yang Jiao
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, China
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, Collaborative Innovation Center of Hematology, Suzhou, China
| | - Jiawei Ren
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, China
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
| | - Shichang Xie
- Key Laboratory of Alkene-Carbon Fibers-Based Technology & Application for Detection of Major Infectious Diseases, MOE Key Laboratory of Geriatric Diseases and Immunology, Cancer Institute, Suzhou Medical College, Soochow University, Suzhou, China
| | - Nan Yuan
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, China
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
| | - Jiaqi Shen
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, China
- Department of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Cyrus Tang Hematology Center, Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Soochow University, Suzhou, China
| | - Huafang Yin
- The Affiliated Jiangyin People’s Hospital of Nantong University, Jiangyin, China
| | - Jian Wang
- The Affiliated Jiangyin People’s Hospital of Nantong University, Jiangyin, China
| | - Hongjuan Guo
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, China
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
| | - Jianping Cao
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, China
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
| | - Xin Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Food Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Depei Wu
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, China
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, Collaborative Innovation Center of Hematology, Suzhou, China
- Department of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Cyrus Tang Hematology Center, Soochow University, Suzhou, China
- Institute of Blood and Marrow Transplantation, Soochow University, Suzhou, China
| | - Zhemin Zhou
- Key Laboratory of Alkene-Carbon Fibers-Based Technology & Application for Detection of Major Infectious Diseases, MOE Key Laboratory of Geriatric Diseases and Immunology, Cancer Institute, Suzhou Medical College, Soochow University, Suzhou, China
- Cancer Institute, Suzhou Medical College, The Second Affiliated Hospital of Soochow University, Suzhou, China
- National Center of Technology Innovation for Biopharmaceuticals, Suzhou Biomedical Industry Innovation Center, Suzhou, China
| | - Xiaofei Qi
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, Collaborative Innovation Center of Hematology, Suzhou, China
- Department of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Cyrus Tang Hematology Center, Soochow University, Suzhou, China
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5
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Fumagalli A, Castells-Nobau A, Trivedi D, Garre-Olmo J, Puig J, Ramos R, Ramió-Torrentà L, Pérez-Brocal V, Moya A, Swann J, Martin-Garcia E, Maldonado R, Fernández-Real JM, Mayneris-Perxachs J. Archaea methanogens are associated with cognitive performance through the shaping of gut microbiota, butyrate and histidine metabolism. Gut Microbes 2025; 17:2455506. [PMID: 39910065 PMCID: PMC11810085 DOI: 10.1080/19490976.2025.2455506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2024] [Revised: 12/28/2024] [Accepted: 01/13/2025] [Indexed: 02/07/2025] Open
Abstract
The relationship between bacteria, cognitive function and obesity is well established, yet the role of archaeal species remains underexplored. We used shotgun metagenomics and neuropsychological tests to identify microbial species associated with cognition in a discovery cohort (IRONMET, n = 125). Interestingly, methanogen archaeas exhibited the strongest positive associations with cognition, particularly Methanobrevibacter smithii (M. smithii). Stratifying individuals by median-centered log ratios (CLR) of M. smithii (low and high M. smithii groups: LMs and HMs) revealed that HMs exhibited better cognition and distinct gut bacterial profiles (PERMANOVA p = 0.001), characterized by increased levels of Verrucomicrobia, Synergistetes and Lentisphaerae species and reduced levels of Bacteroidetes and Proteobacteria. Several of these species were linked to the cognitive test scores. These findings were replicated in a large-scale validation cohort (Aging Imageomics, n = 942). Functional analyses revealed an enrichment of energy, butyrate, and bile acid metabolism in HMs in both cohorts. Global plasma metabolomics by CIL LC-MS in IRONMET identified an enrichment of methylhistidine, phenylacetate, alpha-linolenic and linoleic acid, and secondary bile acid metabolism associated with increased levels of 3-methylhistidine, phenylacetylgluamine, adrenic acid, and isolithocholic acid in the HMs group. Phenylacetate and linoleic acid metabolism also emerged in the Aging Imageomics cohort performing untargeted HPLC-ESI-MS/MS metabolic profiling, while a targeted bile acid profiling identified again isolithocholic acid as one of the most significant bile acid increased in the HMs. 3-Methylhistidine levels were also associated with intense physical activity in a second validation cohort (IRONMET-CGM, n = 116). Finally, FMT from HMs donors improved cognitive flexibility, reduced weight, and altered SCFAs, histidine-, linoleic acid- and phenylalanine-related metabolites in the dorsal striatum of recipient mice. M. smithii seems to interact with the bacterial ecosystem affecting butyrate, histidine, phenylalanine, and linoleic acid metabolism with a positive impact on cognition, constituting a promising therapeutic target to enhance cognitive performance, especially in subjects with obesity.
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Affiliation(s)
- Andrea Fumagalli
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IDIBGI-CERCA), Girona, Spain
- Integrative Systems Medicine and Biology Group, Girona Biomedical Research Institute (IDIBGI-CERCA), Salt, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III; Madrid, Spain
| | - Anna Castells-Nobau
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IDIBGI-CERCA), Girona, Spain
- Integrative Systems Medicine and Biology Group, Girona Biomedical Research Institute (IDIBGI-CERCA), Salt, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III; Madrid, Spain
| | - Dakshat Trivedi
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Josep Garre-Olmo
- serra-hunter program Department of Nursing, University of Girona, Girona, Spain
| | - Josep Puig
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
- Institute of Diagnostic Imaging (IDI)-Research Unit (IDIR), Parc Sanitari Pere Virgili, Barcelona, Spain
- Medical Imaging, Girona Biomedical Research Institute (IdibGi), Girona, Spain
- Department of Radiology (IDI), Dr. Josep Trueta University Hospital, Girona, Spain
| | - Rafel Ramos
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
- Vascular Health Research Group of Girona (ISV-Girona), Jordi Gol Institute for Primary Care Research (Institut Universitari per a la Recerca en Atenció Primària Jordi Gol I Gorina -IDIAPJGol), Red de Investigación en Cronicidad, Atención Primaria y Promoción de la Salud-RICAPPS- ISCIII Girona Biomedical Research Institute (IDIBGI), Dr. Josep Trueta University Hospital, Girona, Catalonia, Spain
- Research in Vascular Health Group, Girona Biomedical Research Institute (IDIBGI-CERCA), Dr. Josep Trueta University Hospital, Girona, Spain
| | - Lluís Ramió-Torrentà
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
- Neuroimmunology and Multiple Sclerosis Unit, Department of Neurology, Dr. Josep Trueta University Hospital, Girona, Spain
- Neurodegeneration and Neuroinflammation Research Group, IDIBGI-CERCA, Girona, Spain
| | - Vicente Pérez-Brocal
- Area of Genomics and Health, Foundation for the Promotion of Sanitary and Biomedical Research of Valencia Region (FISABIO-Public Health), Valencia, Spain
- Biomedical Research Networking Center for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Andrés Moya
- Area of Genomics and Health, Foundation for the Promotion of Sanitary and Biomedical Research of Valencia Region (FISABIO-Public Health), Valencia, Spain
- Biomedical Research Networking Center for Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and Spanish National Research Council (CSIC), Valencia, Spain
| | - Jonathan Swann
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Elena Martin-Garcia
- Laboratory of Neuropharmacology, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Rafael Maldonado
- Laboratory of Neuropharmacology, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - José Manuel Fernández-Real
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IDIBGI-CERCA), Girona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III; Madrid, Spain
| | - Jordi Mayneris-Perxachs
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Integrative Systems Medicine and Biology Group, Girona Biomedical Research Institute (IDIBGI-CERCA), Salt, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III; Madrid, Spain
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6
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Zou Y, Pu L, Guo A, Li Y, Liu Y, Wang Y, Ding Y, Du X, Guo X, Zhang S, Cai X, Wang S. Helminth reshapes host gut microbiota and immunoregulation by deploying an antimicrobial program of innate immunity. Gut Microbes 2025; 17:2496447. [PMID: 40266093 PMCID: PMC12026035 DOI: 10.1080/19490976.2025.2496447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2025] [Revised: 03/17/2025] [Accepted: 04/11/2025] [Indexed: 04/24/2025] Open
Abstract
Helminths can manipulate their host's gut microbiota, with the expansion of the lactobacilli population being a common feature. This process profoundly influences host immunoregulation, yet the underlying mechanisms remain almost unknown. Using a tissue-dwelling helminth model (larval Echinococcus multilocularis) while validating key findings from other helminth infections, we show that helminths harness the antibacterial program of host innate immunity to transform the host gut microbiome and control gut microbiota-mediated immunity. Using multifaceted techniques, we elucidate that cathelicidin-related antimicrobial peptide (CRAMP), derived from the expanded CD11b+CD206+ macrophages rather than the intestinal epithelial cells, is the key component that enters into the gut ecological system and enhances the fitness of Lactobacillus by selectively killing gram-negative microbes like enterobacteria. Furthermore, through in vitro cell culturing and in vivo dietary intervention experiments, we demonstrate that this regulation from innate immunity is boosted via toll-like receptor signaling by helminth's secretory products, which could be sufficiently tuned down by dietary vitamin D through its receptor and cyp27b1. Importantly, using microbiota-targeted treatment methods, we prove that this signaling bolsters gut microbiota-mediated host intestinal Foxp3+ Treg cell expansion and parasite survival and that therapies targeting this signaling are effective in treating infection. We outline a dietary micronutrient-dependent mechanism by which helminths leverage host innate immunity to edit the host gut microbiome and thereby control immunosuppression precisely.
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Affiliation(s)
- Yang Zou
- State Key Laboratory of Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Lixia Pu
- State Key Laboratory of Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Aijiang Guo
- State Key Laboratory of Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Yaqi Li
- State Key Laboratory of Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Yihui Liu
- State Key Laboratory of Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Yugui Wang
- State Key Laboratory of Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Yingying Ding
- State Key Laboratory of Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Xiaowei Du
- State Key Laboratory of Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Xiaola Guo
- State Key Laboratory of Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Shaohua Zhang
- State Key Laboratory of Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Xuepeng Cai
- State Key Laboratory of Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Shuai Wang
- State Key Laboratory of Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
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7
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Akagbosu CO, McCauley KE, Namasivayam S, Romero-Soto HN, O’Brien W, Bacorn M, Bohrnsen E, Schwarz B, Mistry S, Burns AS, Perez-Chaparro PJ, Chen Q, LaPoint P, Patel A, Krausfeldt LE, Subramanian P, Sellers BA, Cheung F, Apps R, Douagi I, Levy S, Nadler EP, Hourigan SK. Gut microbiome shifts in adolescents after sleeve gastrectomy with increased oral-associated taxa and pro-inflammatory potential. Gut Microbes 2025; 17:2467833. [PMID: 39971742 PMCID: PMC11845021 DOI: 10.1080/19490976.2025.2467833] [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: 09/26/2024] [Revised: 01/30/2025] [Accepted: 02/10/2025] [Indexed: 02/21/2025] Open
Abstract
Bariatric surgery is highly effective in achieving weight loss in children and adolescents with severe obesity, however the underlying mechanisms are incompletely understood, and gut microbiome changes are unknown. Here, we show that adolescents exhibit significant gut microbiome and metabolome shifts several months after laparoscopic vertical sleeve gastrectomy (VSG), with increased alpha diversity and notably with enrichment of oral-associated taxa. To assess causality of the microbiome/metabolome changes in phenotype, pre-VSG and post-VSG stool was transplanted into germ-free mice. Post-VSG stool was not associated with any beneficial outcomes such as adiposity reduction compared pre-VSG stool. However, post-VSG stool exhibited a potentially inflammatory phenotype with increased intestinal Th17 and decreased regulatory T cells. Concomitantly, we found elevated fecal calprotectin and an enrichment of proinflammatory pathways in a subset of adolescents post-VSG. We show that in some adolescents, microbiome changes post-VSG may have inflammatory potential, which may be of importance considering the increased incidence of inflammatory bowel disease post-VSG.
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Affiliation(s)
- Cynthia O. Akagbosu
- Department of Gastroenterology, Weill Cornell Medicine, New York, New York, USA
| | - Kathryn E. McCauley
- Bioinformatics and Computational Biosciences Branch National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Sivaranjani Namasivayam
- Clinical Microbiome Unit, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Hector N. Romero-Soto
- Clinical Microbiome Unit, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Wade O’Brien
- Dartmouth Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Mickayla Bacorn
- Clinical Microbiome Unit, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Eric Bohrnsen
- Research Technologies Branch, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, Division of Intramural Research, Rocky Mountain Laboratories, National Institutes of Health, Hamilton, Montana, USA
| | - Benjamin Schwarz
- Research Technologies Branch, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, Division of Intramural Research, Rocky Mountain Laboratories, National Institutes of Health, Hamilton, Montana, USA
| | - Shreni Mistry
- NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Andrew S. Burns
- NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - P. Juliana Perez-Chaparro
- NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Qing Chen
- Clinical Microbiome Unit, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Phoebe LaPoint
- Clinical Microbiome Unit, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Anal Patel
- Clinical Microbiome Unit, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Lauren E. Krausfeldt
- Bioinformatics and Computational Biosciences Branch National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Poorani Subramanian
- Bioinformatics and Computational Biosciences Branch National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Brian A. Sellers
- NIH Center for Human Immunology, Autoimmunity, and Inflammation (CHI), Bethesda, Maryland, USA
| | - Foo Cheung
- NIH Center for Human Immunology, Autoimmunity, and Inflammation (CHI), Bethesda, Maryland, USA
| | - Richard Apps
- NIH Center for Human Immunology, Autoimmunity, and Inflammation (CHI), Bethesda, Maryland, USA
| | - Iyadh Douagi
- NIH Center for Human Immunology, Autoimmunity, and Inflammation (CHI), Bethesda, Maryland, USA
| | - Shira Levy
- Clinical Microbiome Unit, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Suchitra K. Hourigan
- Clinical Microbiome Unit, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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8
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Nakajima A, Arzamasov AA, Sakanaka M, Murakami R, Kozakai T, Yoshida K, Katoh T, Ojima MN, Hirose J, Nagao S, Xiao JZ, Odamaki T, Rodionov DA, Katayama T. In vitro competition with Bifidobacterium strains impairs potentially pathogenic growth of Clostridium perfringens on 2'-fucosyllactose. Gut Microbes 2025; 17:2478306. [PMID: 40102238 PMCID: PMC11956901 DOI: 10.1080/19490976.2025.2478306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2024] [Revised: 02/23/2025] [Accepted: 03/04/2025] [Indexed: 03/20/2025] Open
Abstract
Fortifying infant formula with human milk oligosaccharides, such as 2'-fucosyllactose (2'-FL), is a global trend. Previous studies have shown the inability of pathogenic gut microbes to utilize 2'-FL. However, the present study demonstrates that the type strain (JCM 1290T) of Clostridium perfringens, a pathobiont species often more prevalent and abundant in the feces of C-section-delivered infants, exhibits potentially pathogenic growth on 2'-FL. The expression of genes for α-toxin, an activator of NLRP3 inflammasome, and ethanolamine ammonia-lyase, a factor responsible for the progression of gas gangrene, was significantly upregulated during 2'-FL assimilation compared to growth on lactose. However, colony-forming unit of C. perfringens JCM 1290T markedly decreased when co-cultivated with selected strains of Bifidobacterium, a taxon frequently detected in the breastfed infant gut. Moreover, during co-cultivation, the expression of virulence-related genes, including the gene for perfringolysin O - another activator of NLRP3 inflammasome - were significantly downregulated, while the lactate oxidation genes were upregulated. This can occur through two different mechanisms: direct competition for 2'-FL between the two organisms, or cross-feeding of lactose, released from 2'-FL by C. perfringens JCM 1290T, to Bifidobacterium. Attenuation of α-toxin production by the selected Bifidobacterium strains was observed to varying extents in 2'-FL-utilizing C. perfringens strains clinically isolated from healthy infants. Our results warrant detailed in vivo studies using animal models with dysbiotic microbiota dominated by various types of C. perfringens strains to further validate the safety of 2'-FL for clinical interventions, particularly on vulnerable preterm infants.
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Affiliation(s)
- Aruto Nakajima
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Aleksandr A. Arzamasov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | | | - Ryuta Murakami
- Innovative Research Institute, Morinaga Milk Industry Co, Ltd, Zama, Kanagawa, Japan
| | - Tomoya Kozakai
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Keisuke Yoshida
- Innovative Research Institute, Morinaga Milk Industry Co, Ltd, Zama, Kanagawa, Japan
| | - Toshihiko Katoh
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Miriam N. Ojima
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Junko Hirose
- Department of Food and Nutrition, Kyoto Women’s University, Kyoto, Japan
| | | | - Jin-Zhong Xiao
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Innovative Research Institute, Morinaga Milk Industry Co, Ltd, Zama, Kanagawa, Japan
| | - Toshitaka Odamaki
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Innovative Research Institute, Morinaga Milk Industry Co, Ltd, Zama, Kanagawa, Japan
| | - Dmitry A. Rodionov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Takane Katayama
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
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9
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Yang Y, Lin W, Li H, Yang F, Bao X, Pan C, Lai L, Lin W, Lin R. Identification of candidate genes affecting egg weight trait of Putian Black duck based on whole genome resequencing. Anim Biotechnol 2025; 36:2503754. [PMID: 40380810 DOI: 10.1080/10495398.2025.2503754] [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: 08/08/2024] [Accepted: 05/05/2025] [Indexed: 05/19/2025]
Abstract
Egg weight is a primary economic trait in poultry breeding. Putian Black duck, an excellent local laying duck breed in Fujian Province, includes two different strains, black feather strain and white feather strain. The white feather strain of Putian Black duck is also known as Putian White duck. Except for the different feather colors, these two strains differ in egg weight. In this study, whole-genome resequencing was conducted on Putian Black duck and Putian White duck to explore the differences in the genetic mechanism of egg weight. LRP8, VLDLR, and LPL were identified as key candidate genes affecting egg weight. Mass spectrometry was used to detect the SNPs of LRP8, VLDLR, and LPL. Result indicates that the SNPs of LRP8, VLDLR, and LPL in both populations exhibited moderate polymorphism, and Putian Black duck possessed higher genetic variation and potential selectivity. Association analysis indicated that in Putian Black duck, four SNPs in the LRP8 gene were significantly associated with egg weight. These loci can be used as molecular markers for improving egg weight in Putian Black duck.
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Affiliation(s)
- Yinhua Yang
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Weilong Lin
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Huihuang Li
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Fan Yang
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Xinguo Bao
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Chengfu Pan
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Lianjie Lai
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Weimin Lin
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Ruiyi Lin
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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10
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Ma L, Lin X, Xu M, Ke X, Liu D, Chen Q. Exploring the biological mechanisms of severe COVID-19 in the elderly: Insights from an aged mouse model. Virulence 2025; 16:2487671. [PMID: 40228062 PMCID: PMC12005417 DOI: 10.1080/21505594.2025.2487671] [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: 09/14/2024] [Revised: 02/04/2025] [Accepted: 03/26/2025] [Indexed: 04/16/2025] Open
Abstract
The elderly population, who have increased susceptibility to severe outcomes, have been particularly impacted by the coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), leading to a global health crisis. However, definitive parameters or mechanisms underlying the severity of COVID-19 in elderly people remain unclear. Thus, this study seeks to elucidate the mechanism behind the increased vulnerability of elderly individuals to severe COVID-19. We employed an aged mouse model with a mouse-adapted SARS-CoV-2 strain to mimic the severe symptoms observed in elderly patients with COVID-19. Comprehensive analyses of the whole lung were performed using transcriptome and proteome sequencing, comparing data from aged and young mice. For transcriptome analysis, bulk RNA sequencing was conducted using an Illumina sequencing platform. Proteomic analysis was performed using mass spectrometry following protein extraction, digestion, and peptide labelling. We analysed the transcriptome and proteome profiles of young and aged mice and discovered that aged mice exhibited elevated baseline levels of inflammation and tissue damage repair. After SARS-CoV-2 infection, aged mice showed increased antiviral and inflammatory responses; however, these responses were weaker than those in young mice, with significant complement and coagulation cascade responses. In summary, our study demonstrates that the increased vulnerability of the elderly to severe COVID-19 may be attributed to an attenuated antiviral response and the overactivation of complement and coagulation cascades. Future research on antiviral and inflammatory responses is likely to yield treatments that reduce the severity of viral respiratory diseases in the elderly.
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Affiliation(s)
- Li Ma
- State Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Xian Lin
- State Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- Hubei Jiangxia Laboratory, Wuhan, China
| | - Meng Xu
- State Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Xianliang Ke
- State Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Di Liu
- State Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Quanjiao Chen
- State Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
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11
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Jiang S, Huang S, Zhang Z, Ma W, Han Z, Song Y, Huo D, Cui W, Zhang J. Gut microbiota drives structural variation of exogenous probiotics to enhance colonization. Gut Microbes 2025; 17:2503371. [PMID: 40349120 PMCID: PMC12068336 DOI: 10.1080/19490976.2025.2503371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2025] [Revised: 04/26/2025] [Accepted: 05/02/2025] [Indexed: 05/14/2025] Open
Abstract
Probiotics encounter colonization resistance from native gut microbiomes, affecting their effectiveness. Genetic engineering of probiotics lacks universal applicability, as gut microbiotas are highly individualized. Here, we employed probiotic Lactiplantibacillus plantarum HNU082 (Lp082) to test whether Lp082 gut-adapted mutants can resolve colonization resistance in a new gut environment. Relying on culture-based methods and metagenomics, two distinct evolutionary clades of Lp082 in mice gut were observed, where one clade, which acquired more mutations, exhibited a longer survival time. However, these Lp082 isolates carrying many single nucleotide variants (SNVs) still exhibited phenotypic inconsistencies, with 13 strains of enhanced acid resistance. Thus, nanopore sequencing was proposed to identify structural variations (SVs). Among them, 12 strains had the Cro/C1-type HTH DNA-binding domain insertion, which enhanced growth and reproduction under bile salt stress, thereby increasing colonization time and quantity in the gut. The gut domestication process can drive probiotics to undergo many SNVs and SVs, thereby enhancing their colonization ability, which provides new insights into the colonization mechanisms and offers an ecology-based strategy.
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Affiliation(s)
- Shuaiming Jiang
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, China
| | - Shi Huang
- Faculty of Dentistry, The University of Hong Kong, Hong Kong, SAR, China
| | - Zeng Zhang
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, China
| | - Wenyao Ma
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, China
| | - Zhe Han
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, China
| | - Yuan Song
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, China
| | - Dongxue Huo
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, China
| | - Weipeng Cui
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, China
| | - Jiachao Zhang
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, China
- Collaborative Innovation Center of One Health, Hainan University, Haikou, Hainan, China
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12
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Wang X, Li S, Ou R, Pang W, Wang Y, Zhang Y, Lin Y, Yang C, Chen W, Lei C, Zeng G, Zhou W, Wang Y, Yin J, Zhang H, Jin X, Zhang Y. Wide-spectrum profiling of plasma cell-free RNA and the potential for health-monitoring. RNA Biol 2025; 22:1-15. [PMID: 40110666 PMCID: PMC11970758 DOI: 10.1080/15476286.2025.2481736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2024] [Revised: 02/10/2025] [Accepted: 03/13/2025] [Indexed: 03/22/2025] Open
Abstract
Circulating cell-free RNA (cfRNA) has emerged as a promising analyte for disease detection. However, the comprehensive profiling of diverse cfRNA types remains under-characterized. Here, we applied a new wide-spectrum cfRNA sequencing method and simultaneously captured rRNA, tRNA, mRNA, miRNA, lncRNA and all mitochondrial RNA. The cfRNA compositions, size distributions and highly abundant cfRNA genes were analysed for each type of cfRNA. We depicted the cfRNA cell types of origin profiles of 66 generally healthy individuals and found that BMI showed a significant impact on the kidney-derived cfRNA proportion. Three individuals with some liver problems were identified because of relatively high levels of hepatocyte-specific cfRNA. The abundance levels of different genes and RNA types, including mRNA, miRNA and lncRNA, were significantly correlated with the liver function test results. The genes of individual cfRNA variances were enriched in pathways associated with common diseases such as liver diseases, virus infections, cancers and metabolic diseases. This study provided a profiling of cfRNA and displayed the potential of cfRNA as a biomarker in health monitoring.
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Affiliation(s)
- Xinxin Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
- BGI Research, Shenzhen, China
| | - Shaogang Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
- BGI Research, Shenzhen, China
| | | | - Wending Pang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
- BGI Research, Shenzhen, China
| | | | - Yifan Zhang
- BGI Research, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yu Lin
- BGI Research, Shenzhen, China
| | - Changlin Yang
- BGI Research, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wei Chen
- BGI Research, Shenzhen, China
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
| | | | - Guodan Zeng
- BGI Research, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | | | | | | | | | - Xin Jin
- BGI Research, Shenzhen, China
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
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13
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You H, Yang B, Liu H, Wu W, Yu F, Lin N, Yang W, Hu B, Liu Y, Zou H, Hao S, Xiao Y, Xu T, Jiang Y. Unravelling distinct patterns of metagenomic surveillance and respiratory microbiota between two P1 genotypes of Mycoplasma pneumoniae. Emerg Microbes Infect 2025; 14:2449087. [PMID: 39760260 PMCID: PMC11730683 DOI: 10.1080/22221751.2024.2449087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 12/04/2024] [Accepted: 12/29/2024] [Indexed: 01/07/2025]
Abstract
To unravel distinct patterns of metagenomic surveillance and respiratory microbiota between Mycoplasma pneumoniae (M. pneumoniae) P1-1 and P1-2 and to explore the impact of the COVID-19 pandemic on epidemiological features, we conducted a multicentre retrospective study which spanned 90,886 pneumonia patients, among which 3164 cases M. pneumoniae were identified. Our findings revealed a concurrent outbreak of M. pneumoniae, with the positivity rate rising sharply to 9.62% from July 2023, compared to the 0.16% to 4.06% positivity rate observed during the 2020-2022 COVID-19 pandemic. P1-1 had a higher odds ratio of co-detecting opportunistic pathogens. However, no significant differences were observed in the co-detection odds ratio between children and other age groups in P1-2. This study is the first to demonstrate differences in relative abundance, diversity of respiratory microbiota and co-detection rate of opportunistic pathogen between M. pneumoniae P1-1 and P1-2. Through bronchoalveolar lavage (BAL) metagenomic and host transcriptomic analyses, we identified variations in co-detection rates of M. pneumoniae P1-1 genotype with opportunistic pathogens like S. pneumoniae, alterations in respiratory microbiota composition, lung inflammation, and disruption of ciliary function. Consistent with the results of host transcriptome, we found that P1-1 infections were associated with significantly higher rates of requiring respiratory support and mechanical ventilation compared to P1-2 infections (Fisher's exact test, p-value = 0.035/0.004). Our study provides preliminary evidence of clinical severity between M. pneumoniae strains, underscoring the need for ongoing research and development of targeted therapeutic strategies.
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Affiliation(s)
- Hailong You
- Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, Jilin, People’s Republic of China
| | - Bin Yang
- Center for Infectious Diseases, Vision Medicals Co., Ltd, Guangzhou, Guangdong, People’s Republic of China
| | - Huifang Liu
- Center for Infectious Diseases, Vision Medicals Co., Ltd, Guangzhou, Guangdong, People’s Republic of China
| | - Wencai Wu
- Center for Infectious Diseases, Vision Medicals Co., Ltd, Guangzhou, Guangdong, People’s Republic of China
| | - Fei Yu
- Medical Research Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, People’s Republic of China
| | - Nan Lin
- Department of Environmental Health, School of Public Health, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - WenJiao Yang
- Center for Infectious Diseases, Vision Medicals Co., Ltd, Guangzhou, Guangdong, People’s Republic of China
| | - Bingxue Hu
- Center for Infectious Diseases, Vision Medicals Co., Ltd, Guangzhou, Guangdong, People’s Republic of China
| | - Yong Liu
- Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, Jilin, People’s Republic of China
| | - Hongyan Zou
- Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, Jilin, People’s Republic of China
| | - Sijia Hao
- Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, Jilin, People’s Republic of China
| | - Yunping Xiao
- Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, Jilin, People’s Republic of China
| | - Teng Xu
- Center for Infectious Diseases, Vision Medicals Co., Ltd, Guangzhou, Guangdong, People’s Republic of China
| | - Yanfang Jiang
- Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, Jilin, People’s Republic of China
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14
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Chen A, Teng C, Wei J, Wu X, Zhang H, Chen P, Cai D, Qian H, Zhu H, Zheng X, Chen X. Gut microbial dysbiosis exacerbates long-term cognitive impairments by promoting intestinal dysfunction and neuroinflammation following neonatal hypoxia-ischemia. Gut Microbes 2025; 17:2471015. [PMID: 40008452 PMCID: PMC11866968 DOI: 10.1080/19490976.2025.2471015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 01/12/2025] [Accepted: 02/18/2025] [Indexed: 02/27/2025] Open
Abstract
Neonatal hypoxic-ischemic brain damage (HIBD) is considered as a major cause of long-term cognitive impairments in newborns. It has been demonstrated that gut microbiota is closely associated with the prognosis of various neurological disorders. However, the role of microbiota-gut-brain axis on cognitive function following neonatal HIBD remains elusive. In this experiment, the correlation analysis supported the involvement of gut microbial changes following hypoxic-ischemic (HI) insult in the development of long-term cognitive impairments. Subsequent experiment revealed the involvement of the intestinal dysfunction in the hippocampal neuroinflammation and synaptic injury. In causal relationship validation experiments, fecal microbiota transplantation (FMT) from cognitively normal rats could restore gut microbial composition, improve intestinal dysfunction, reduce the serum levels of lipopolysaccharides (LPS) and inflammatory mediators, and alleviate neuroinflammation, synaptic damage and cognitive impairments in neonatal HIBD recipient rats. Conversely, the FMT from neonatal HIBD rats could induce above adverse pathological changes in the normal recipient rats. Moreover, oral administration of anti-inflammatory agent dexamethasone (DEX) exhibited the potential to alleviate these detrimental effects in neonatal HIBD rats, with the efficacy being partly reliant on gut microbiota. Further experiment on the potential molecular mechanisms using RNA sequencing indicated a significant increase in the toll-like receptor 4 (TLR4) gene in the intestinal tissues of neonatal HIBD rats. Additionally, the interventions such as TLR4 inhibitor TLR4-IN-C34 administration, FMT, and oral DEX were demonstrated to modulate intestinal function by inhibiting the LPS/TLR4 signaling pathway, thereby exerting neuroprotective effects. Collectively, these findings underscore the contribution of gut microbial dysbiosis post HI insult in activating the LPS/TLR4 signaling pathway, triggering intestinal inflammation and dysfunction, exacerbating systemic inflammation, and consequently worsening synaptic and cognitive impairments in neonatal HIBD rats. Hence, rectifying gut microbial dysbiosis or regulating intestinal function may represent a promising strategy for alleviating long-term cognitive impairments in neonates affected by HIBD.
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Affiliation(s)
- Andi Chen
- Shengli Clinical Medical College of Fujian Medical University, Department of Anesthesiology, Fujian Provincial Hospital, Fuzhou University Affiliated Provincial Hospital, Fuzhou, China
| | - Chengqian Teng
- Shengli Clinical Medical College of Fujian Medical University, Department of Anesthesiology, Fujian Provincial Hospital, Fuzhou University Affiliated Provincial Hospital, Fuzhou, China
| | - Jianjie Wei
- Shengli Clinical Medical College of Fujian Medical University, Department of Anesthesiology, Fujian Provincial Hospital, Fuzhou University Affiliated Provincial Hospital, Fuzhou, China
| | - Xuyang Wu
- Shengli Clinical Medical College of Fujian Medical University, Department of Anesthesiology, Fujian Provincial Hospital, Fuzhou University Affiliated Provincial Hospital, Fuzhou, China
| | - Honghong Zhang
- Shengli Clinical Medical College of Fujian Medical University, Department of Anesthesiology, Fujian Provincial Hospital, Fuzhou University Affiliated Provincial Hospital, Fuzhou, China
| | - Pinzhong Chen
- Shengli Clinical Medical College of Fujian Medical University, Department of Anesthesiology, Fujian Provincial Hospital, Fuzhou University Affiliated Provincial Hospital, Fuzhou, China
| | - Dingliang Cai
- Shengli Clinical Medical College of Fujian Medical University, Department of Anesthesiology, Fujian Provincial Hospital, Fuzhou University Affiliated Provincial Hospital, Fuzhou, China
| | - Haitao Qian
- Shengli Clinical Medical College of Fujian Medical University, Department of Anesthesiology, Fujian Provincial Hospital, Fuzhou University Affiliated Provincial Hospital, Fuzhou, China
| | - Hui Zhu
- Department of Neonatal Intensive Care Unit, Fujian Provincial Hospital, Fuzhou University Affiliated Provincial Hospital, Fuzhou, China
| | - Xiaochun Zheng
- Shengli Clinical Medical College of Fujian Medical University, Department of Anesthesiology, Fujian Provincial Hospital, Fuzhou University Affiliated Provincial Hospital, Fuzhou, China
| | - Xiaohui Chen
- Shengli Clinical Medical College of Fujian Medical University, Department of Anesthesiology, Fujian Provincial Hospital, Fuzhou University Affiliated Provincial Hospital, Fuzhou, China
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15
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Tahira AC, Gomes MPB, Freire MH, Muxfeldt M, Prosdocimi F, Passos YM, Sena Amaral M, Felix Valadão LP, Rangel LP, Silva JL, Verjovski-Almeida S, Cordeiro Y. RNA-seq analyses reveal the relevance of RNAs involved in ribosomal complex to induce mammalian prion protein aggregation and phase separation in vitro. RNA Biol 2025; 22:1-16. [PMID: 40438940 PMCID: PMC12123958 DOI: 10.1080/15476286.2025.2508107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/01/2025] [Accepted: 05/01/2025] [Indexed: 06/02/2025] Open
Abstract
Conformational conversion of cellular prion protein (PrPC) into infectious PrP (PrPSc) is one of the most intriguing processes in modern Biology. It is well accepted that this transition is catalysed by one or more cofactors that lower the energy barrier between the different PrP forms. Among potential candidates, RNA molecules are strong contenders. Our group has pursued nucleic acids, both DNA and RNA, capable of inducing PrP misfolding, aggregation, and, more recently, phase separation, a process proposed to precede aggregation in degenerative disorders. We found that the interaction between recombinant PrP (rPrP) and total RNA extracted from neuroblastoma cells (N2aRNA) results in significant structural alterations. Here, we use rPrP:N2aRNA as a model to search for RNAs capable of inducing full-length murine rPrP phase separation and/or aggregation. N2aRNA was incubated with rPrP and after that, RNA-seq analysis was conducted with RNAs isolated from the insoluble material using two different protocols. We analysed thousands of RNA-seq reads, most of which represented ribosomal RNA molecules. The set of recovered molecules is heterogeneous; nevertheless, three low-complexity consensus motifs within the sequences of RNAs involved in ribosomal complex were identified as significantly enriched in the RNAs bound to rPrP, suggesting that a population of RNAs is responsible for inducing PrP phase transitions. We hypothesize that RNA transcripts enriched in a set of low complexity motif sequences with predicted structural similarities can be involved in PrPC binding. This interaction would lead to phase separation and, ultimately, result in aggregation into scrapie-like species, in a stoichiometry-dependent manner.
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Affiliation(s)
- Ana C. Tahira
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brasil
| | - Mariana P. B. Gomes
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
- Fundação Oswaldo Cruz, Instituto de Tecnologia em Imunobiológicos, Rio de Janeiro, Brasil
| | - Maria Heloisa Freire
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Marcelly Muxfeldt
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Francisco Prosdocimi
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Yulli M. Passos
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | | | | | - Luciana P. Rangel
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Jerson L. Silva
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
- D’Or Institute for Research and Education (IDOR), Rio de Janeiro, RJ, Brazil
| | - Sergio Verjovski-Almeida
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brasil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brasil
| | - Yraima Cordeiro
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
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16
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Li H, Liu H, Wu H, Guo C, Zuo W, Zheng Y, Deng X, Xu J, Wang Y, Wang Z, Lu B, Hou B, Cao B. Reading of human acute immune dynamics in omicron SARS-CoV-2 breakthrough infection. Emerg Microbes Infect 2025; 14:2494705. [PMID: 40231451 PMCID: PMC12064115 DOI: 10.1080/22221751.2025.2494705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2024] [Revised: 03/19/2025] [Accepted: 04/13/2025] [Indexed: 04/16/2025]
Abstract
The dynamics of the immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) breakthrough infections remain unclear, particularly when compared to responses in naive individuals. In this longitudinal prospective cohort study, 13 participants were recruited. Peripheral blood samples were collected every other day until day 7 after symptom onset. Transcriptome sequencing, single-cell sequencing, T-cell receptor (TCR) sequencing, B-cell receptor (BCR) sequencing, Olink proteomics, and antigen-antibody binding experiments were then performed. During the incubation periods of breakthrough infections, peripheral blood exhibited type 2 cytokine response, which shifted to type 1 cytokine response upon symptom onset. Plasma cytokine levels of C-X-C motif chemokine ligand 10, monocyte chemoattractant protein-1, interferon-γ, and interleukin-6 show larger changes in breakthrough infections than naïve infections. The inflammatory response in breakthrough infections rapidly subsided, returning to homeostasis by day 5 after symptom onset. Notably, the levels of monocyte-derived S100A8/A9, previously considered a marker of severe disease, physiologically significantly increased in the early stages of mild cases and persisted until day 7, suggesting a specific biological function. Longitudinal tracking also revealed that antibodies anti-Receptor Binding Domain (anti-RBD) in breakthrough infections significantly increased by day 7 after symptom onset, whereas cytotoxic T lymphocytes appeared by day 5. This study presents a reference for interpreting the immunological response to breakthrough infectious disease in humans.
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Affiliation(s)
- Haibo Li
- National Center for Respiratory Medicine; State Key Laboratory of Respiratory Health and Multimorbidity; National Clinical Research Center for Respiratory Diseases; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences; Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, People’s Republic of China
- New Cornerstone Science Laboratory, Beijing, People’s Republic of China
| | - Hongyu Liu
- National Center for Respiratory Medicine; State Key Laboratory of Respiratory Health and Multimorbidity; National Clinical Research Center for Respiratory Diseases; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences; Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, People’s Republic of China
- Department of Respiratory Medicine, Capital Medical University, Beijing, People’s Republic of China
| | - Hongping Wu
- National Center for Respiratory Medicine; State Key Laboratory of Respiratory Health and Multimorbidity; National Clinical Research Center for Respiratory Diseases; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences; Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, People’s Republic of China
| | - Chang Guo
- Changping National Laboratory (CPNL), Beijing, People’s Republic of China
| | - Wenting Zuo
- National Center for Respiratory Medicine; State Key Laboratory of Respiratory Health and Multimorbidity; National Clinical Research Center for Respiratory Diseases; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences; Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, People’s Republic of China
| | - Ying Zheng
- Department of Respiratory Medicine, Capital Medical University, Beijing, People’s Republic of China
| | - Xiaoyan Deng
- Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, People’s Republic of China
| | - Jiuyang Xu
- National Center for Respiratory Medicine; State Key Laboratory of Respiratory Health and Multimorbidity; National Clinical Research Center for Respiratory Diseases; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences; Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, People’s Republic of China
| | - Yeming Wang
- National Center for Respiratory Medicine; State Key Laboratory of Respiratory Health and Multimorbidity; National Clinical Research Center for Respiratory Diseases; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences; Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, People’s Republic of China
| | - Zai Wang
- Institute of Clinical Medical Sciences, China-Japan Friendship Hospital, Beijing, People’s Republic of China
| | - Binghuai Lu
- National Center for Respiratory Medicine; State Key Laboratory of Respiratory Health and Multimorbidity; National Clinical Research Center for Respiratory Diseases; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences; Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, People’s Republic of China
| | - Baidong Hou
- State Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Bin Cao
- National Center for Respiratory Medicine; State Key Laboratory of Respiratory Health and Multimorbidity; National Clinical Research Center for Respiratory Diseases; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences; Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, People’s Republic of China
- New Cornerstone Science Laboratory, Beijing, People’s Republic of China
- Department of Respiratory Medicine, Capital Medical University, Beijing, People’s Republic of China
- Institute of Clinical Medical Sciences, China-Japan Friendship Hospital, Beijing, People’s Republic of China
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17
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Batalha MA, LeCroy MN, Lin J, Peters BA, Qi Q, Wang Z, Wang T, Gallo LC, Talavera GA, McClain AC, Thyagarajan B, Daviglus ML, Hou L, Llabre M, Cai J, Kaplan RC, Isasi CR. Life-course socioeconomic position and the gut microbiome in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL). Gut Microbes 2025; 17:2479772. [PMID: 40102030 DOI: 10.1080/19490976.2025.2479772] [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: 07/10/2024] [Revised: 02/03/2025] [Accepted: 03/10/2025] [Indexed: 03/20/2025] Open
Abstract
Socioeconomic position (SEP) in childhood and beyond may influence the gut microbiome, with implications for disease risk. Studies evaluating the relationship between life-course SEP and the gut microbiome are sparse, particularly among Hispanic/Latino individuals, who have a high prevalence of low SEP. We use the Hispanic Community Health Study/Study of Latinos (HCHS/SOL), a population-based cohort study conducted in four field centers in the United States (U.S.), to evaluate the association between life-course SEP and gut microbiome composition. Life-course SEP indicators included parental education (proxy of childhood SEP), current SEP (n = 2174), and childhood (n = 988) and current economic hardship (n = 994). Shotgun sequencing was performed on stool samples. Analysis of Compositions of Microbiomes was used to identify associations of life-course SEP indicators with gut microbiome species and functions. Parental education and current SEP were associated with the overall gut microbiome composition; however, parental education and current education explained more the gut microbiome variance than the current SEP. A lower parental education and current SEP were associated with a lower abundance of species from genus Bacteroides. In stratified analysis by nativity, we found similar findings mainly among foreign-born participants. Early-life SEP may have long-term effects on gut microbiome composition underscoring another biological mechanism linking early childhood factors to adult disease.
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Affiliation(s)
- Monica A Batalha
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Madison N LeCroy
- Department of Population Health, NYU Grossman School of Medicine, New York, NY, USA
| | - Juan Lin
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Brandilyn A Peters
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Zheng Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Tao Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Linda C Gallo
- Department of Psychology, San Diego State University, San Diego, CA, USA
| | - Gregory A Talavera
- Department of Psychology, San Diego State University, San Diego, CA, USA
| | - Amanda C McClain
- School of Exercise and Nutritional Sciences, San Diego State University, San Diego, CA, USA
| | - Bharat Thyagarajan
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Martha L Daviglus
- Institute for Minority Health Research, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University, Chicago, IL, USA
| | - Maria Llabre
- Department of Psychology, University of Miami, Miami, FL, USA
| | - Jianwen Cai
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Robert C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Carmen R Isasi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
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18
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Dong J, Mao Z, Li H, Wang R, Wang Y, Jia H, Li J, Liu Q, Zhang C, Liao X, Liu D, Ma H, Tian C. MTD: A cloud-based omics database and interactive platform for Myceliophthora thermophila. Synth Syst Biotechnol 2025; 10:783-793. [PMID: 40276250 PMCID: PMC12018684 DOI: 10.1016/j.synbio.2025.04.001] [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] [Received: 01/06/2025] [Revised: 03/05/2025] [Accepted: 04/02/2025] [Indexed: 04/26/2025] Open
Abstract
Nowadays, biological databases are playing an increasingly critical role in biological research. Myceliophthora thermophila is an excellent thermophilic fungal chassis for industrial enzyme production and plant biomass-based chemical synthesis. The lack of a dedicated public database has made access to and reanalysis of M. thermophila data difficult. To bridge this gap, we developed MTD (https://mtd.biodesign.ac.cn/), a cloud-based omics database and interactive platform for M. thermophila. MTD integrates comprehensive genome annotations, sequence-based predictions, transcriptome data, curated experimental descriptions, and bioinformatics analysis tools, offering a comprehensive, one-stop solution with a 'top-down' search strategy to streamline M. thermophila research. The platform supports data reproduction, rapid querying, and in-depth mining of existing transcriptome datasets. Based on analyses using data and tools in MTD, we identified shifts in metabolic allocation in a glucoamylase hyperproduction strain of M. thermophila, highlighting changes in fatty acid biosynthesis and amino acids biosynthesis pathways, which provide new insights into the underlying phenotypic alterations. As a pioneering resource, MTD marks a key advancement in M. thermophila research and sets the model for developing similar databases for other species.
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Affiliation(s)
- Jiacheng Dong
- State Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- Haihe Laboratory of Synthetic Biology, Tianjin, 300308, China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Zhitao Mao
- Biodesign Center, State Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Haoran Li
- Biodesign Center, State Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Ruoyu Wang
- Biodesign Center, State Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Yutao Wang
- State Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Haokai Jia
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
- College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jingen Li
- State Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Qian Liu
- State Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Chenglin Zhang
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Xiaoping Liao
- Biodesign Center, State Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Defei Liu
- State Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Hongwu Ma
- Biodesign Center, State Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Chaoguang Tian
- State Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
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19
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Kang D, Lu H, Kang T, Zhang Y, Ge Z, Zhang L, Peng Y. Heterogeneous microstructure induces floatation in high-rate anammox granules. WATER RESEARCH X 2025; 28:100319. [PMID: 40028193 PMCID: PMC11871469 DOI: 10.1016/j.wroa.2025.100319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2024] [Revised: 12/11/2024] [Accepted: 02/09/2025] [Indexed: 03/05/2025]
Abstract
The floatation of anammox granules can be a serious challenge in practical wastewater treatment, as it can deteriorate reactor performance and cause bacterial loss. To deepen the understanding of floatation mechanism, in this study, both the floating (F-AnGS) and settling anammox granules (S-AnGS) from a high-rate anammox reactor were comparatively investigated. F-AnGS demonstrated 1.6 times higher specific anammox activity compared to S-AnGS, but only 65 % of produced gas could be successfully released, as quantified by anaerobic respirometry. In addition to the overall EPS accumulation, F-AnGS exhibited a heterogeneous microstructure distinct from that of S-AnGS, as revealed by 3D X-ray microscopic imaging at the single granule level. The heterogeneous distribution of EPS, which can form a dense surface layer, was the main cause for granule floatation. The heterogeneous microstructure of F-AnGS can reduce the distance between microorganisms and enhance the metabolic interaction between anammox bacteria and heterotrophs. The abundance of community members did not have a significant variation, but the functional genes related to anammox and partial denitrification pathway were significantly increased, indicating the enhanced nitrite loop in F-AnGS. This study proposed new structural insights into mechanism of anammox granule floatation, suggesting the appropriate activity control of granule-based anammox process.
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Affiliation(s)
- Da Kang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Department of Environmental Engineering, Beijing University of Technology, PR China
| | - Huifeng Lu
- Zhejiang Water Healer Environmental Technology Co., Ltd, Hangzhou, PR China
| | - Tingting Kang
- Zhejiang Water Healer Environmental Technology Co., Ltd, Hangzhou, PR China
| | - Yihan Zhang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Department of Environmental Engineering, Beijing University of Technology, PR China
| | - Zheng Ge
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Department of Environmental Engineering, Beijing University of Technology, PR China
| | - Liang Zhang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Department of Environmental Engineering, Beijing University of Technology, PR China
| | - Yongzhen Peng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Department of Environmental Engineering, Beijing University of Technology, PR China
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20
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Kim CW, Kim HJ, Kang I, Ku KB, Kim Y, Park JH, Lim J, Kang BH, Park WH, La J, Chang S, Hwang I, Kim M, Ahn S, Lee HK. Gut dysbiosis from high-salt diet promotes glioma via propionate-mediated TGF-β activation. J Exp Med 2025; 222:e20241135. [PMID: 40402148 PMCID: PMC12097148 DOI: 10.1084/jem.20241135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 03/08/2025] [Accepted: 05/05/2025] [Indexed: 05/23/2025] Open
Abstract
The purpose of this study is to investigate the impact of a high-salt diet (HSD), which is commonly found in Western countries, on the progression of glioma. Our research shows that the alterations in gut microbiota caused by an HSD facilitated the development of glioma. Mice fed an HSD have elevated levels of intestinal propionate, which accelerated the growth of glioma cells. We also find that propionate supplementation enhanced the response of glioma cells to low oxygen levels. Moreover, we identify a link between TGF-β signaling, response to low oxygen levels, and invasion-related pathways. Propionate treatment increases the expression of HIF-1α, leading to an increase in TGF-β1 production. Additionally, propionate treatment promotes glioma cell invasion through TGF-β signaling. Our findings suggest that an HSD-induced increase in propionate plays a crucial role in glioma progression by facilitating invasion through the hypoxic response and TGF-β signaling pathways, thereby establishing a significant connection between gut microbiota and the progression of glioma.
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Affiliation(s)
- Chae Won Kim
- Laboratory of Host Defenses, Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- KAIST Life Science Institute, KAIST, Daejeon, Republic of Korea
| | - Hyun-Jin Kim
- Laboratory of Host Defenses, Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- KAIST Life Science Institute, KAIST, Daejeon, Republic of Korea
| | - In Kang
- Laboratory of Host Defenses, Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, Republic of Korea
| | - Keun Bon Ku
- Laboratory of Host Defenses, Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, Republic of Korea
- Department of Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Yumin Kim
- Laboratory of Host Defenses, Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Jang Hyun Park
- Laboratory of Host Defenses, Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- KAIST Life Science Institute, KAIST, Daejeon, Republic of Korea
| | - Juhee Lim
- Laboratory of Host Defenses, Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, Republic of Korea
| | - Byeong Hoon Kang
- Laboratory of Host Defenses, Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, Republic of Korea
| | - Won Hyung Park
- Laboratory of Host Defenses, Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, Republic of Korea
| | - Jeongwoo La
- Laboratory of Host Defenses, Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, Republic of Korea
| | - Sungwoo Chang
- Laboratory of Host Defenses, Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Inju Hwang
- Laboratory of Host Defenses, Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, Republic of Korea
| | - Minji Kim
- Laboratory of Host Defenses, Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, Republic of Korea
| | - Stephen Ahn
- Department of Neurosurgery, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Heung Kyu Lee
- Laboratory of Host Defenses, Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
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21
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Zhang Y, He K, Zhang C, Dang H, Hei J, Zhang Y, Chen P, Zhang Z, Yang Y, Wang Z, Yang X, Zhang L, Yu Y. Atlas of temporal molecular pathological alterations after traumatic brain injury based on RNA-Seq. Exp Neurol 2025; 390:115270. [PMID: 40268159 DOI: 10.1016/j.expneurol.2025.115270] [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: 12/22/2024] [Revised: 04/01/2025] [Accepted: 04/20/2025] [Indexed: 04/25/2025]
Abstract
Traumatic brain injury (TBI) involves diverse molecular pathological alterations and biological processes in a temporally dynamic manner. However, current knowledge on the various processes during the acute phase of TBI is still rather limited. RNA-seq analysis was performed on brain tissues from C57/BL6 mice at 10 time points(0 h, 1 h, 2 h, 3 h, 4 h, 6 h, 12 h, 1d, 3d, and 7d) following TBI modeling. Subsequently, a bioinformatics approach, Weighted Gene Co-expression Network Analysis (WGCNA), was employed to identify characteristic modules, which were then validated using the Mfuzz method. Pathway enrichment analysis was conducted on WGCNA module genes, and hub genes were screened using the STRING database. After exploring the various potential pathways and expression patterns (neuroinflammation, cognition, gliosis and myelin regeneration etc.), we focus on pyroptosis, a inflammatory cell death influencing immune response, for in-depth analysis. RT-qPCR, Western blot(WB) and Immunofluorescence(IF) were used to validate the hub genes and key pyroptosis-related genes(Casp1, Casp11, GSDMD). Additionally, single-cell RNA sequencing data at 7 day post injury(dpi) was also used to validate the expression of the identified hub genes. Our approach to intensive transcriptomic analysis comprehensively reveals the temporal molecular pathological alterations during TBI progression. Pyroptosis may be a key mechanism in the neuroinflammatory process. Intervention strategies targeting specific molecular pathways may offer novel approach for the treatment of TBI.
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Affiliation(s)
- Yulian Zhang
- Department of Neurosurgery, China-Japan Friendship Hospital, Beijing 100029, China
| | - Kun He
- Department of Neurosurgery, China-Japan Friendship Hospital, Beijing 100029, China; Peking University China-Japan Friendship School of Clinical Medicine, Beijing 100029, China
| | - Chuanpeng Zhang
- Department of Neurosurgery, China-Japan Friendship Hospital, Beijing 100029, China; Peking University China-Japan Friendship School of Clinical Medicine, Beijing 100029, China
| | - Hanhan Dang
- Department of Neurosurgery, China-Japan Friendship Hospital, Beijing 100029, China; China-Japan Friendship Hospital (Institute of Clinical Medical Sciences), Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100029, China
| | - Junru Hei
- Department of Neurosurgery, The First Medical Center, Chinese PLA General Hospital, Beijing 100039, China
| | - Yunsheng Zhang
- Department of Neurosurgery, China-Japan Friendship Hospital, Beijing 100029, China; Peking University China-Japan Friendship School of Clinical Medicine, Beijing 100029, China
| | - Pengyu Chen
- Department of Neurosurgery, China-Japan Friendship Hospital, Beijing 100029, China; China-Japan Friendship Hospital (Institute of Clinical Medical Sciences), Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100029, China
| | - Ze Zhang
- Department of Neurosurgery, China-Japan Friendship Hospital, Beijing 100029, China; China-Japan Friendship Hospital (Institute of Clinical Medical Sciences), Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100029, China
| | - Yanbo Yang
- Department of Neurosurgery, China-Japan Friendship Hospital, Beijing 100029, China; Peking University China-Japan Friendship School of Clinical Medicine, Beijing 100029, China
| | - Zixi Wang
- Department of Neurosurgery, China-Japan Friendship Hospital, Beijing 100029, China; Peking University China-Japan Friendship School of Clinical Medicine, Beijing 100029, China
| | - Xu Yang
- Department of Neurosurgery, China-Japan Friendship Hospital, Beijing 100029, China; Peking University China-Japan Friendship School of Clinical Medicine, Beijing 100029, China
| | - Li Zhang
- Department of Neurosurgery, China-Japan Friendship Hospital, Beijing 100029, China; Peking University China-Japan Friendship School of Clinical Medicine, Beijing 100029, China; China-Japan Friendship Hospital (Institute of Clinical Medical Sciences), Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100029, China
| | - Yanbing Yu
- Department of Neurosurgery, China-Japan Friendship Hospital, Beijing 100029, China; Peking University China-Japan Friendship School of Clinical Medicine, Beijing 100029, China; China-Japan Friendship Hospital (Institute of Clinical Medical Sciences), Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100029, China.
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22
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Peng Q, Quan L, Zheng H, Li J, Xie G. Analyzing the contribution of top-down and bottom-up methods to the construction of synthetic microbial communities in Jiuyao. Food Microbiol 2025; 129:104759. [PMID: 40086988 DOI: 10.1016/j.fm.2025.104759] [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: 10/10/2024] [Revised: 01/16/2025] [Accepted: 02/19/2025] [Indexed: 03/16/2025]
Abstract
The construction of synthetic microbial communities is a crucial strategy for improving the stability of microbial populations and the quality of fermented foods. Jiuyao, an essential saccharification and fermentation starter in Huangjiu production, was the focus of this study. Using metagenomics combined with culture-dependent methods, we identified 11 microbial species involved in Huangjiu fermentation. Through metagenomic analysis and simulated fermentation, Rhizopus delemar, Rhizopus microspores, Rhizopus stolonife, Rhizopus azygosporus, Saccharomycopsis fibuligera, Saccharomyces cerevisiae, Wickerhamomyces anomalus and Pediococcus pentosaceus were determined to be the core microbial species driving the Jiuyao fermentation process. A synthetic microbial community was constructed based on these species, successfully reproducing the flavor and sensory qualities of Huangjiu while enhancing fermentation efficiency. This study provides valuable insights into the functional roles of Jiuyao-associated microbes and offers a framework for improving microbial community stability and fermentation quality in Huangjiu production.
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Affiliation(s)
- Qi Peng
- National Engineering Research Center for Chinese CRW (Branch Center), School of Life and Environmental Sciences, Shaoxing University, 900 Chengnan Road, Shaoxing, 312000, China
| | - Leping Quan
- National Engineering Research Center for Chinese CRW (Branch Center), School of Life and Environmental Sciences, Shaoxing University, 900 Chengnan Road, Shaoxing, 312000, China
| | - Huajun Zheng
- National Engineering Research Center for Chinese CRW (Branch Center), School of Life and Environmental Sciences, Shaoxing University, 900 Chengnan Road, Shaoxing, 312000, China
| | - Jiachen Li
- National Engineering Research Center for Chinese CRW (Branch Center), School of Life and Environmental Sciences, Shaoxing University, 900 Chengnan Road, Shaoxing, 312000, China
| | - Guangfa Xie
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, College of Biology and Environmental Engineering, Zhejiang Shuren University, Hangzhou, 310015, China.
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23
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Kothe CI, Renault P. Metagenomic driven isolation of poorly culturable species in food. Food Microbiol 2025; 129:104722. [PMID: 40086981 DOI: 10.1016/j.fm.2025.104722] [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: 10/30/2024] [Revised: 01/02/2025] [Accepted: 01/02/2025] [Indexed: 03/16/2025]
Abstract
Although isolating microorganisms from food microbiota may appear less challenging than from the gut or environmental sources, recovering all representative species from food remains a difficult task. Here, we showed by metagenomic analysis that several abundant species had escaped isolation in a previous study of ten cheeses, including several previously uncharacterized species. This highlights the ongoing challenge of achieving a comprehensive recovery of microbes from food. To address this gap, we designed a novel strategy integrating metagenomics-based probes targeting the species of interest, coupled with an incremental culturing approach using pooled samples. As proof of concept, we applied this strategy to two cheeses containing species that were not isolated in our previous study, with the objective of isolating all species present at levels above 2% and, in particular, potential novel food species. Through this approach, we successfully performed the targeted isolation of two Psychrobacter and two Vibrio species from the first cheese, and four Halomonas and two Pseudoalteromonas species from the second one. Notably, P. undina and V. litoralis represented, as far as we know, the first cheese isolates characterized for these species. However, we were unable to isolate a novel species of Pseudoalteromonas, with no characterized representative to date, and Marinomonas foliarum, previously isolated from marine environment. Using metagenome-assembled genomes (MAGs) and metagenomic analysis, we discussed the possible reasons for their non-recovery. Finally, this strategy offers a promising approach for isolating a set of strains representative of the microbial diversity present in food ecosystems. These isolates can serve as a basis for investigating their roles in the communities, their impact on product development, safety implications and their potential in the development of starter cultures.
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Affiliation(s)
- Caroline Isabel Kothe
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Pierre Renault
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France.
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24
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Guan L, Wang P, Li Y, Zhang S. FERONIA interacts with NPL4 to regulate immunity gene mRNA nucleocytoplasmic transport in response to plant immunity. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2025; 357:112545. [PMID: 40348341 DOI: 10.1016/j.plantsci.2025.112545] [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: 12/06/2024] [Revised: 05/04/2025] [Accepted: 05/05/2025] [Indexed: 05/14/2025]
Abstract
Nucleocytoplasmic transport plays a critical role in the activation of immune mechanisms in plant cells. Fluorescence imaging analysis indicated that a high concentration of rapid alkalinization factor (RALF) suppresses the immune response and can induce nuclear envelope (NE) shape deformation. This phenomenon depends on the receptor kinase FERONIA (FER). Consistently, bacterial infection also affects NE shape. This study presents evidence that FER displays functional interactions with NPL4 and that phosphorylated NPL4 promotes its stability. We reported the identification and characterization of the nuclear localization protein NPL4, which is directly involved in general mRNA nuclear export. FER and NPL4 mutations both affected rhizosphere Pseudomonas colonization levels, suggesting that the interactions between FER and NPL4 are largely indispensable for regulating rhizosphere Pseudomonas colonization levels. In addition, NPL4 altered the mRNA nucleocytoplasmic distribution of immune genes in conjunction with the function of RALF-FER in the suppression of plant immunity. In brief, NPL4, which is downstream of FER is required for innate immunity and mRNA nuclear accumulation of resistance genes in Arabidopsis. Overall, through the analysis of RALF-FER and the nuclear localization protein NPL4, this work provides novel insights into the mRNA nucleocytoplasmic transport of immune genes and plant health.
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Affiliation(s)
- Li Guan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, PR China.
| | - Peilong Wang
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, 334 Xueshan Road, Wenzhou 325005, PR China
| | - Yongliang Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, PR China
| | - Sufang Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, PR China
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25
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Li B, Liang C, Xu B, Song P, Liu D, Zhang J, Gu H, Jiang F, Gao H, Cai Z, Zhang T. Extreme winter environment dominates gut microbiota and metabolome of white-lipped deer. Microbiol Res 2025; 297:128182. [PMID: 40252261 DOI: 10.1016/j.micres.2025.128182] [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: 07/25/2024] [Revised: 03/23/2025] [Accepted: 04/10/2025] [Indexed: 04/21/2025]
Abstract
Qinghai-Tibet Plateau (QTP) is marked by harsh environments that drive the evolution of unique nutrient metabolism mechanism in indigenous animal gut microbiotas. Yet, responses of these microbiotas to different extreme environments remain poorly understood. White-lipped deer (Przewalskium albirostris), a native endangered species in the QTP, serves as an ideal model to study how gut microbiotas adapt to season and human disturbances. Here, a multi-omics integrated analysis of 16S rRNA, metagenomics, and untargeted metabolomics was performed to investigate the composition, function, and metabolic characteristics of gut microbiota in White-lipped deer across different seasons and living environments. Our results revealed that extreme winter environment dominated the composition, function, and metabolism of gut microbiota in white-lipped deer. The white-lipped deer exhibited an enriched gut microbiota associated with producing short-chain fatty acids in winter, with core feature genera including norank_o_Rhodospirillales, Rikenellaceae_RC9_gut_group, and unclassified_c_Clostridia. However, potential pathogenic bacteria and few short-chain fatty acid producers, with core feature genera including norank_f_p-2534-18B5_gut_group, Cellulosilyticum, and Paeniclostridium, showed enrichment in captivity. Pathways associated with carbohydrate metabolism, amino acid metabolism, and immune regulation showed enrichment in winter group as an adaptation to the cold and food scarcity. Among these, Rikenellaceae_RC9_gut_group and unclassified_c_Clostridia contributed significantly to these metabolic pathways. The gut microbiota of white-lipped deer exhibited enrichment in pathways related to intestinal inflammation and enhanced immune regulation to alleviate the stress of captivity. Among these, norank_f_p-2534-18B5_gut_group contributed the most to these pathways. Butyric, valeric, and valproic acids were significantly more abundant in the winter group, while 3-hydroxybutyric and (S)-beta-aminoisobutyric acids were higher in the captive group. Furthermore, enriched metabolites and associated pathways in both groups further supported the inferences on metagenomic functions. This study confirms the key role of specific gut microbiota in adapting to high-altitude winters and anthropogenic disturbances, emphasizing its importance for environmental resilience in wild, high-altitude mammals.
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Affiliation(s)
- Bin Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China; Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Chengbo Liang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China; Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Bo Xu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China; Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Pengfei Song
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China; Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | | | | | - Haifeng Gu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China; Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Feng Jiang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China; Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Hongmei Gao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China; Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Zhenyuan Cai
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China; Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China.
| | - Tongzuo Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China; Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China.
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26
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Liu S, Zheng Y, Cui B, Yang J, Yuan B, Cao Y, Zhao Z, Sun Z, Wang Q, Yang X, Pan W, He C. Gut microbiota-derived butyrate alleviates the impairment of mice intestinal integrity caused by Toxoplasma gondii infection. Life Sci 2025; 374:123709. [PMID: 40368048 DOI: 10.1016/j.lfs.2025.123709] [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: 01/24/2025] [Revised: 05/04/2025] [Accepted: 05/09/2025] [Indexed: 05/16/2025]
Abstract
Chronic infection with Toxoplasma gondii (T. gondii) results in severe damages to the integrity of intestinal barrier, however, both the underlying mechanism and feasible intervention strategies are still little known. Here, we found that both the chronic infection of T. gondii and transplanting gut microbiota from T. gondii-infected mice severely impaired the mice intestinal integrity, which was characterized by significantly decreased thickness of inner mucus layer and down-regulated expression of three tight junction proteins Occludin, ZO-1, and Claudin (p < 0.05). Moreover, T. gondii infection also led to mice intestinal microbiota dysbiosis, especially butyrate-producing bacteria, and significantly changed the expression of several senescence-associated markers, including 6- and 7- fold upregulation for P16, P21, and 6-fold downregulation for Lamin B1 at mRNA levels, and 2-fold downregulation for β-galactosidase at protein levels (p < 0.05). Interestingly, subsequent administration with dietary butyrate could alleviate T. gondii-induced intestinal integrity impairment and cell senescence, revealing a significant increase of the inner mucus layer thickness (p < 0.001), and a remarkable decrease in P16, P21, β-galactosidase expression levels while an upregulation of Lamin B1 expression (p < 0.05). Taken together, our study revealed that T. gondii-induced dysbiosis of gut microbiota, especially butyrate-producing bacteria, contributes to the intestinal impairment, potentially via promoting cell senescence. In addition, administration with the metabolite, butyrate, could be a promising therapeutic measure against T. gondii infection.
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Affiliation(s)
- Shuni Liu
- Jiangsu Key Laboratory of Immunity and Metabolism, Xuzhou Medical University, China; The First Clinical Medical College, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yutao Zheng
- Jiangsu Key Laboratory of Immunity and Metabolism, Xuzhou Medical University, China; School of Stomatology, Xuzhou Medical University, Xuzhou, China
| | - Bingqian Cui
- Jiangsu Key Laboratory of Immunity and Metabolism, Xuzhou Medical University, China; The First Clinical Medical College, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Jiayi Yang
- Jiangsu Key Laboratory of Immunity and Metabolism, Xuzhou Medical University, China; The First Clinical Medical College, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Bohui Yuan
- Jiangsu Key Laboratory of Immunity and Metabolism, Xuzhou Medical University, China
| | - Yuhan Cao
- The Second Clinical Medical College, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Zimu Zhao
- The First Clinical Medical College, Xuzhou Medical University, Xuzhou, Jiangsu, China; Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Zhuo Sun
- Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Qingling Wang
- Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Xiaoying Yang
- Jiangsu Key Laboratory of Immunity and Metabolism, Xuzhou Medical University, China; Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Xuzhou Medical University, China
| | - Wei Pan
- Jiangsu Key Laboratory of Immunity and Metabolism, Xuzhou Medical University, China; Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Xuzhou Medical University, China.
| | - Cheng He
- Jiangsu Key Laboratory of Immunity and Metabolism, Xuzhou Medical University, China; Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Xuzhou Medical University, China.
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27
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Chen Y, Wang R, Zhu Z, Subedi N, Jiang X, Jing M, Huang L. Phylogenomic analyses revealed a new lineage of house mouse (Mus musculus) in Gyirong Basin of Xizang Autonomous Region, China. Mol Phylogenet Evol 2025; 209:108370. [PMID: 40339673 DOI: 10.1016/j.ympev.2025.108370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2024] [Revised: 04/03/2025] [Accepted: 05/04/2025] [Indexed: 05/10/2025]
Abstract
In the present study, we collected 20 individuals and 12 individuals of wild mice from the Gyirong Basin of Xizang Autonomous Region in China and Sudurpashchim in Nepal. Phylogeny and genetic structure inferred from different types of genomic markers suggest that these samples all belong to Mus musculus, among which individuals from Gyirong Basin represent a new genomic lineage (named as M. m. gyirongus), and samples from Sudurpashchim represent an intermediate population between the central population and M. m. castaneus. M. m. gyirongus, along with M. m. domesticus and M. m. musculus, differentiated from the central population compactly during ∼ 272,000-251,000 years ago in the interglacial period. Three lineages all experienced continuous population decline before ∼ 70,000 years ago. Then, they underwent population fluctuations at different periods that might have been impacted by climate changes, migration history, and human activities. Genes related to the structure and function of neural synapses, reproduction and development, regulation of cell cycle and carcinogenesis, and immune response have undergone positive selection in the genome of M. m. gyirongus. The discovery of M. m. gyirongus not only helps us to better understand the evolutionary history of M. musculus, but also provides new regional resources for breeding novel laboratory mouse strains.
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Affiliation(s)
- Yingjie Chen
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Rongguo Wang
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Zhongxu Zhu
- Key Laboratory of Genetic Evolution and Animal Models & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Naresh Subedi
- National Trust for Nature Conservation, Lalitpur, Nepal
| | - Xuelong Jiang
- Key Laboratory of Genetic Evolution and Animal Models & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
| | - Meidong Jing
- School of Life Sciences, Nantong University, Nantong 226019, China.
| | - Ling Huang
- School of Life Sciences, Nantong University, Nantong 226019, China.
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28
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Zhu Y, Zhang X, Tao W, Yang S, Qi H, Zhou Q, Su W, Zhang Y, Dong Y, Gan Y, Lei C, Zhang A. Mitigating the risk of antibiotic resistance and pathogenic bacteria in swine waste: The role of ectopic fermentation beds. JOURNAL OF HAZARDOUS MATERIALS 2025; 492:138221. [PMID: 40220395 DOI: 10.1016/j.jhazmat.2025.138221] [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: 01/09/2025] [Revised: 03/21/2025] [Accepted: 04/07/2025] [Indexed: 04/14/2025]
Abstract
The ectopic fermentation bed (EFB) is used to recycle animal waste, but the fate and dynamic change of antibiotic resistance genes (ARGs) with biocide or heavy metal resistance genes (B/MRGs) and pathogens remain unclear. We performed metagenomic sequencing on 129 samples to study the resistome and bacteriome in pig feces from 24 farms, comparing these profiles with EFBs from five farms, and one farm's EFB was monitored for 154 days. Results showed pig feces from different cities (Chengdu, Meishan, and Chongqing) shared 284 of 311 ARG subtypes, with over 70 % being high-risk ARGs, and 106 of 114 pathogenic bacteria. Swine farms were heavily contaminated with co-occurrences of risky ARGs, B/MRGs, and pathogenic hosts, particularly Escherichia coli and Streptococcus suis being hosts of multidrug ARGs. The application of EFBs markedly mitigated these risks in feces, showing a 3.09-fold decrease in high-risk ARGs, a 72.22 % reduction in B/MRGs, a 3.95-fold drop in prioritized pathogens, an 89.09 % decline in the relative abundance of pig pathogens, and a simplification of their correlation networks and co-occurrence patterns. A mantel analysis revealed that metal contents (Fe, Mn, and Cu) and time influenced pathogen and ARG profiles. Pathogens, ARGs, and risk ARGs exhibited periodic variations, peaking at days 14, 84, and 154, with 70-day intervals. This study provides a comprehensive assessment of the risks associated with pig feces and EFBs and demonstrates that EFBs reduce ARG risks by inhibiting their associations with B/MRGs and pathogens. These findings can help guide and improve the management of antimicrobial resistance and pathogenic contaminants in EFB applications to reduce environmental pollution.
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Affiliation(s)
- Yixiao Zhu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Xialan Zhang
- Central Agricultural Broadcasting and Television School (Banan, Chongqing), Chongqing 401320, China
| | - Weilai Tao
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Shujian Yang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Haoxuan Qi
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Quan Zhou
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Wen Su
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yanhang Zhang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yongyi Dong
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yumeng Gan
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Changwei Lei
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Anyun Zhang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China.
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29
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Peng H, Zhang Z, Kang X, Zhang Y, Zhang H, Wang Y, Yang D, Zhang J, Wang Y, Cui L, Zhu YG, Ju F. Unveiling gut microbiota and metabolic functions contributed to polyvinyl chloride degradation in Spodoptera frugiperda larvae. JOURNAL OF HAZARDOUS MATERIALS 2025; 492:138209. [PMID: 40222058 DOI: 10.1016/j.jhazmat.2025.138209] [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: 02/20/2025] [Revised: 04/04/2025] [Accepted: 04/06/2025] [Indexed: 04/15/2025]
Abstract
The accumulation of synthetic plastic waste, particularly polyvinyl chloride (PVC), threatens ecosystems globally. While microbial biodegradation represents a sustainable solution, limited effective PVC-degrading microbial bioresources have been identified. Here, we investigated the gut microbiota of Spodoptera frugiperda larvae, revealing a consistent microbial profile dominated by Enterococcus in both gut contents and tissues. PVC film feeding induced significant microbiota shifts, with functional parallels to PVC powder-fed Tenebrio molitor larvae despite taxonomic divergence. Through enzyme-centric analysis, we found an Enterococcus casseliflavus strain from the gut of S. frugiperda larvae could encode a NAD-dependent oxidoreductase that directly dechlorinates additive-free PVC, representing the first case of enzymatic polymer dechlorination. This enzyme reduced PVC molecular weight (Mn: 12.02 %; Mw: 14.07 %) and notably liberated chloride ions (6.48 mg/L with NADH as a co-factor). Our findings demonstrate the PVC-degrading capacity of S. frugiperda gut microbiota and reveal its dechlorination mechanism, offering an enzymatic candidate for developing novel biocatalysts and engineered microbial strains for enhanced biodegradation. By unravelling insect-associated microbes and enzymes, this work lays a theoretical foundation for their application potentials in sustainable PVC wastes upcycling and microplastic remediation.
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Affiliation(s)
- Haoran Peng
- Research Center for Industries of the Future, School of Engineering, Westlake University, Hangzhou 310030, China; Zhejiang Provincial Key Laboratory of Intelligent Low-Carbon Biosynthesis, Hangzhou 310030, China; Westlake Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, Hangzhou, Zhejiang 310030, China
| | - Zhe Zhang
- Research Center for Industries of the Future, School of Engineering, Westlake University, Hangzhou 310030, China; Zhejiang Provincial Key Laboratory of Intelligent Low-Carbon Biosynthesis, Hangzhou 310030, China; Westlake Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, Hangzhou, Zhejiang 310030, China
| | - Xiaoxi Kang
- Research Center for Industries of the Future, School of Engineering, Westlake University, Hangzhou 310030, China; Zhejiang Provincial Key Laboratory of Intelligent Low-Carbon Biosynthesis, Hangzhou 310030, China
| | - Yunhua Zhang
- Research Center for Industries of the Future, School of Engineering, Westlake University, Hangzhou 310030, China; Zhejiang Provincial Key Laboratory of Intelligent Low-Carbon Biosynthesis, Hangzhou 310030, China; Westlake Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, Hangzhou, Zhejiang 310030, China
| | - Huilin Zhang
- Research Center for Industries of the Future, School of Engineering, Westlake University, Hangzhou 310030, China; Zhejiang Provincial Key Laboratory of Intelligent Low-Carbon Biosynthesis, Hangzhou 310030, China
| | - Yuxuan Wang
- Westlake Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, Hangzhou, Zhejiang 310030, China
| | - Dongchen Yang
- College of Plant Protection, Hebei Agricultural University, Baoding 071000, China
| | - Jinlin Zhang
- College of Plant Protection, Hebei Agricultural University, Baoding 071000, China
| | - Yajie Wang
- Westlake Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, Hangzhou, Zhejiang 310030, China
| | - Li Cui
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-environmental Science, Chinese Academy of Sciences, Beijing 100085, China
| | - Yong-Guan Zhu
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-environmental Science, Chinese Academy of Sciences, Beijing 100085, China
| | - Feng Ju
- Research Center for Industries of the Future, School of Engineering, Westlake University, Hangzhou 310030, China; Zhejiang Provincial Key Laboratory of Intelligent Low-Carbon Biosynthesis, Hangzhou 310030, China; Westlake Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, Hangzhou, Zhejiang 310030, China; Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, Hangzhou 310024, China.
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30
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Ma JY, Liu JH, Chen CZ, Zhang YZ, Guo ZS, Song MP, Jiang F, Chai ZT, Li Z, Lv SX, Zhen YJ, Wang L, Liang ZL, Jiang ZY. Characteristics of microbial carbon pump in the sediment of kelp aquaculture zone and its contribution to recalcitrant dissolved organic carbon turnover: insights into metabolic patterns and ecological functions. ENVIRONMENTAL RESEARCH 2025; 277:121559. [PMID: 40228693 DOI: 10.1016/j.envres.2025.121559] [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: 01/15/2025] [Revised: 03/29/2025] [Accepted: 04/05/2025] [Indexed: 04/16/2025]
Abstract
The study delves into the microbial carbon pump (MCP) within the sediments of kelp aquaculture zones, focusing on its influence on the turnover of recalcitrant dissolved organic carbon (RDOC). Following kelp harvest, significant alterations in the microbial community structure were noted, with a decrease in complexity and heterogeneity within co-occurrence networks potentially impacting RDOC production efficiency. Metabolic models constructed identified four key microbial lineages crucial for RDOC turnover, with their abundance observed to decrease post-harvest. Analysis of metabolic complementarity revealed that RDOC-degrading microorganisms exhibit broad substrate diversity and are engaged in specific resource exchange patterns, with cross-feeding interactions possibly enhancing the ecological efficiency of the MCP. Notably, the degradation of RDOC was found not to deplete the RDOC pool; as aromatic compounds break down, new ones are released into the environment, thus supporting the renewal of the RDOC pool. The research highlights the pivotal role of microbial communities in RDOC turnover and offers fresh insights into their cross-feeding behavior related to RDOC cycling, providing valuable data to support the future development and application of MCP theory.
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Affiliation(s)
- Jun-Yang Ma
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong, 266237, PR China; Marine College, Shandong University, Weihai, Shandong, 264209, PR China; Key Laboratory of Modern Marine Ranching Technology of Weihai, Weihai, 264209, Shandong, PR China
| | - Ji-Hua Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong, 266237, PR China
| | - Cheng-Zhuang Chen
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Yi-Ze Zhang
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Zhan-Sheng Guo
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China; Key Laboratory of Modern Marine Ranching Technology of Weihai, Weihai, 264209, Shandong, PR China
| | - Min-Peng Song
- Yantai Vocational College, Yantai, 264670, Shandong, PR China
| | - Feng Jiang
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China; Key Laboratory of Modern Marine Ranching Technology of Weihai, Weihai, 264209, Shandong, PR China
| | - Zi-Tong Chai
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China; Key Laboratory of Modern Marine Ranching Technology of Weihai, Weihai, 264209, Shandong, PR China
| | - Zhu Li
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China; Key Laboratory of Modern Marine Ranching Technology of Weihai, Weihai, 264209, Shandong, PR China
| | - Su-Xian Lv
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China; Key Laboratory of Modern Marine Ranching Technology of Weihai, Weihai, 264209, Shandong, PR China
| | - Yu-Jiao Zhen
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China; Key Laboratory of Modern Marine Ranching Technology of Weihai, Weihai, 264209, Shandong, PR China
| | - Lu Wang
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China; Key Laboratory of Modern Marine Ranching Technology of Weihai, Weihai, 264209, Shandong, PR China
| | - Zhen-Lin Liang
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China; Key Laboratory of Modern Marine Ranching Technology of Weihai, Weihai, 264209, Shandong, PR China
| | - Zhao-Yang Jiang
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China; Key Laboratory of Modern Marine Ranching Technology of Weihai, Weihai, 264209, Shandong, PR China.
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31
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Thomson R, Le C, Wang L, Batstone DJ, Zhou Y, Oehmen A. Higher order volatile fatty acid metabolism and atypical polyhydroxyalkanoate production in fermentation-enhanced biological phosphorus removal. WATER RESEARCH 2025; 280:123503. [PMID: 40121909 DOI: 10.1016/j.watres.2025.123503] [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: 05/03/2024] [Revised: 03/11/2025] [Accepted: 03/13/2025] [Indexed: 03/25/2025]
Abstract
Enhanced biological phosphorus removal (EBPR) is an established wastewater treatment process, but its wider implementation has been limited by factors like high temperature and low carbon availability. Fermentation-enhanced EBPR (F-EBPR) processes have shown promise in addressing these limitations, but the underlying mechanisms are not fully understood. This study investigates the metabolism of higher order (C4-5) volatile fatty acids (VFAs) in F-EBPR systems using a combination of carbon isotope labelling and shotgun metagenomic sequencing analyses. Results show that butyrate (HBu) uptake leads to the formation of both typical (C4-5) and atypical (C6+) polyhydroxyalkanoates (PHAs) through a combination ofβ-oxidation and standard condensation pathways, while the putative role of HBu oxidisers were identified relative to substrate composition in F-EBPR processes. Metagenomic analysis reveals the presence of genes required for higher order VFA metabolism in both polyphosphate accumulating organisms (PAOs) and glycogen accumulating organisms (GAOs). This study also highlights the limitations of current models in describing F-EBPR processes and emphasises the need for improved models that account for higher order VFA metabolism and microbial community dynamics.
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Affiliation(s)
- R Thomson
- School of Chemical Engineering, University of Queensland, St Lucia QLD 4072, Australia
| | - C Le
- Asian School of the Environment, Nanyang Technological University, 637141, Singapore
| | - L Wang
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201600, PR China
| | - D J Batstone
- Australian Centre for Water and Environmental Biotechnology, University of Queensland, St Lucia QLD 4072, Australia
| | - Y Zhou
- Advanced Environmental Biotechnology Center, Nanyang Technological University, 637141, Singapore.
| | - A Oehmen
- School of Chemical Engineering, University of Queensland, St Lucia QLD 4072, Australia.
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32
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Cheng Y, Zheng X, Jiang Y, Xiao Q, Luo Q, Ding Y. Key genes and microbial ecological clusters involved in organophosphate ester degradation in agricultural fields of a typical watershed in southwest China. JOURNAL OF HAZARDOUS MATERIALS 2025; 492:138076. [PMID: 40209409 DOI: 10.1016/j.jhazmat.2025.138076] [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: 11/23/2024] [Revised: 03/06/2025] [Accepted: 03/24/2025] [Indexed: 04/12/2025]
Abstract
Organophosphate esters (OPEs) are widely used as flame retardants and plasticizers, and they have raised global concern due to their persistence, bioaccumulation, and potential toxicity. However, OPE contamination characteristics and microbial degradation mechanisms in agricultural soils remain poorly understood. This study investigated agricultural soils from the riparian zone of the Anning River Basin in southwest China. The concentrations of 12 OPEs were determined using gas chromatography-tandem mass spectrometry. The results revealed that the total OPE concentration was moderate, with triethyl phosphate being the most abundant compound. Metagenomic techniques and Bayesian linear regression analysis were employed in combination with the Kyoto Encyclopedia of Genes and Genomes database to identify potential degradation pathways for triethyl phosphate and tris (2-chloroethyl) phosphate. The phoA, phoB, phoD, and glpQ genes, which encode phosphatases, catalyze ester bond cleavage, thereby facilitating the degradation of OPEs. Further microbial interaction network analysis identified core OPE-degrading microorganisms, including Pimelobacter simplex, Nocardioides sp. JS614, Nocardioides daphniae, and Methylocystis heyeri. Additionally, neutral community models indicated that environmental selection drives microbial community structure. In conclusion, this study provides an in-depth understanding of OPE contamination and its microbial degradation mechanisms in agricultural soils, offering theoretical insights for pollution management and remediation strategies.
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Affiliation(s)
- Yu Cheng
- College of Geography, China West Normal University, Nanchong 637009, PR China; Sichuan Provincial Engineering Laboratory of Monitoring and Control for Soil Erosion on Dry Valleys, China West Normal University, Nanchong 637009, PR China
| | - Xuehao Zheng
- College of Geography, China West Normal University, Nanchong 637009, PR China; Sichuan Provincial Engineering Laboratory of Monitoring and Control for Soil Erosion on Dry Valleys, China West Normal University, Nanchong 637009, PR China; Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, PR China.
| | - Yukun Jiang
- Key Laboratory of Ecological Restoration of Regional Contaminated Environment, Ministry of Education, College of Environment, Shenyang University, Shenyang 110044, China
| | - Qiang Xiao
- Sichuan Provincial Engineering Laboratory of Monitoring and Control for Soil Erosion on Dry Valleys, China West Normal University, Nanchong 637009, PR China
| | - Qing Luo
- Key Laboratory of Ecological Restoration of Regional Contaminated Environment, Ministry of Education, College of Environment, Shenyang University, Shenyang 110044, China.
| | - Yongzhen Ding
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, PR China.
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Matsumoto M, Yoshida M, Oya T, Tsuneyama K, Matsumoto M, Yoshida H. Role of PRC2 in the stochastic expression of Aire target genes and development of mimetic cells in the thymus. J Exp Med 2025; 222:e20240817. [PMID: 40244172 PMCID: PMC12005117 DOI: 10.1084/jem.20240817] [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: 05/09/2024] [Revised: 10/10/2024] [Accepted: 03/11/2025] [Indexed: 04/18/2025] Open
Abstract
The transcriptional targets of Aire and the mechanisms controlling their expression in medullary thymic epithelial cells (mTECs) need to be clarified to understand Aire's tolerogenic function. By using a multi-omics single-cell approach coupled with deep scRNA-seq, we examined how Aire controls the transcription of a wide variety of genes in a small fraction of Aire-expressing cells. We found that chromatin repression by PRC2 is an important step for Aire to achieve stochastic gene expression. Aire unleashed the silenced chromatin configuration caused by PRC2, thereby increasing the expression of its functional targets. Besides this preconditioning for Aire's gene induction, we demonstrated that PRC2 also controls the composition of mTECs that mimic the developmental trait of peripheral tissues, i.e., mimetic cells. Of note, this action of PRC2 was independent of Aire and it was more apparent than Aire. Thus, our study uncovered the essential role of polycomb complex for Aire-mediated promiscuous gene expression and the development of mimetic cells.
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Affiliation(s)
- Minoru Matsumoto
- Department of Molecular Pathology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Masaki Yoshida
- YCI Laboratory for Immunological Transcriptomics, RIKEN Center for Integrative Medical Science, Yokohama, Japan
| | - Takeshi Oya
- Department of Molecular Pathology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Koichi Tsuneyama
- Department of Pathology and Laboratory Medicine, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Mitsuru Matsumoto
- Division of Molecular Immunology, Institute for Enzyme Research, Tokushima University, Tokushima, Japan
| | - Hideyuki Yoshida
- YCI Laboratory for Immunological Transcriptomics, RIKEN Center for Integrative Medical Science, Yokohama, Japan
- Department of Endocrinology, Diabetes and Metabolism, Kitasato University School of Medicine, Sagamihara, Japan
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Guo M, Wu Y, Huang H, Li S, Zhao L, Cao J, Wang C. Revealing the critical role of rare bacterial communities in shaping antibiotic resistance genes in saline soils through metagenomic analysis. JOURNAL OF HAZARDOUS MATERIALS 2025; 491:137848. [PMID: 40068396 DOI: 10.1016/j.jhazmat.2025.137848] [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: 10/29/2024] [Revised: 02/19/2025] [Accepted: 03/03/2025] [Indexed: 05/15/2025]
Abstract
Salinity is considered one of the basic abiotic factors influencing the diversity and distribution of antibiotic resistance genes (ARGs) in soils, yet little is known about the distribution and driving factors of ARGs in naturally saline soils. In this study, metagenomic analysis was conducted to explore the intricate dynamics among soil salinity, microbial community structure and ARGs propagation, with a particular focus on the key contribution of rare potential-hosts of ARGs in light and heavy saline soils. The findings revealed that salinity was significantly negatively correlated with the abundance of ARGs, light saline soils hosted a greater abundance of ARGs than high saline soils, with particularly significant enrichment in genes conferring resistance to multidrug, vancomycin, bacitracin and tetracenomycin C. Proteobacteria and Actinobacteria were identified as primary hosts for ARGs. Notably, rare potential hosts of ARGs play a crucial role in shaping the abundance of ARGs despite their low relative abundance (0.85 %), significantly influencing the relative abundance of ARGs in light and heavy saline soils. The average degree of rare potential-hosts of ARGs was found to be higher in light saline soils (average degree = 45.729 and 25.923 in light and heavy saline soils, respectively), and there was stronger interaction connected between microorganisms (edges = 35,760 and 20,259 in light and heavy saline soils, respectively). Also, microbial community niche width and niche overlap of rare potential-hosts of ARGs in light saline soils were significantly greater than that in heavy saline soils. This work emphasizes the importance of bacterial communities of rare potential-hosts of ARGs on antibiotic resistome, and provides advanced insights into the fate and dissemination of ARGs in saline soils.
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Affiliation(s)
- Mengyao Guo
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing 100193, China; State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193 China
| | - Yafen Wu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing 100193, China; State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193 China
| | - Huiying Huang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing 100193, China; State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193 China
| | - Siping Li
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing 100193, China; State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193 China
| | - Lei Zhao
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing 100193, China; State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193 China
| | - Jia Cao
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing 100193, China; State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193 China.
| | - Chong Wang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing 100193, China; State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193 China
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Wang L, Jiang Y, Hao Y, Yu L, Zhao S, Wu H, Long X, Zhang Z, Zhao T, Geng S, Guan X. Integrated transcriptomics and metabolomics analyses reveal jasmonic acid metabolic pathways for improving the chilling tolerance in cotton seedlings. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2025; 224:109935. [PMID: 40286456 DOI: 10.1016/j.plaphy.2025.109935] [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: 02/12/2025] [Revised: 04/04/2025] [Accepted: 04/17/2025] [Indexed: 04/29/2025]
Abstract
Cotton (Gossypium spp.) originated in tropical and subtropical regions, spreading to higher latitudes through domestication while retaining thermophilic characteristics. Xinjiang, a major cotton-producing area in China, frequently experiences 'late spring cold snaps' due to its location, causing chilling injury during critical sowing periods. Current research on cotton chilling stress primarily focuses on physiological studies such as evaluations of chilling stress and biochemical indices but lacks systematic investigation into the difference among varieties. Phenotypic screening across seed germination, cotyledon, and seedling stages identified upland cotton (Gossypium hirsutum) cultivar, Junmian1 exhibits superior cold tolerance relative to the sensitive genotype C1470. Under chilling stress, Junmian1 protects chloroplasts and other cellular structures in its first true leaf to survive the chilling stress. Weighted gene co-expression network analysis (WGCNA) analysis pinpointed Module Brown as a chilling-tolerance responsive hub, with subsequent validation via virus-induced gene silencing (VIGS) confirming the regulatory roles of GhRBL (Ribulose-bisphosphate carboxylase), GhGI (GIGANTEA), and lncRNA MSTR.1631 in cold tolerance. Additionally, integrated metabolomic and transcriptomic analyses demonstrated that jasmonic acid plays a crucial role in enhancing cotton's chilling tolerance at seedling stage. The primary difference in chilling tolerance between Junmian1 and C1470 is attributed to the signaling efficiency of the jasmonic acid synthesis and metabolism pathways. These findings establish JA metabolic engineering as a viable approach for enhancing cold resilience in early-stage cotton seedlings.
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Affiliation(s)
- Luyao Wang
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Zhenzhou Road, Yazhou District, Sanya, Hainan, 572025, China
| | - Yaping Jiang
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Zhenzhou Road, Yazhou District, Sanya, Hainan, 572025, China; Zhejiang Key Laboratory of Crop Germplasm Innovation and Utilization, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yupeng Hao
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Zhenzhou Road, Yazhou District, Sanya, Hainan, 572025, China; Zhejiang Key Laboratory of Crop Germplasm Innovation and Utilization, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Li Yu
- Zhejiang Key Laboratory of Crop Germplasm Innovation and Utilization, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Shengjun Zhao
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Zhenzhou Road, Yazhou District, Sanya, Hainan, 572025, China; Zhejiang Key Laboratory of Crop Germplasm Innovation and Utilization, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Hongyu Wu
- Zhejiang Key Laboratory of Crop Germplasm Innovation and Utilization, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Xuan Long
- Zhejiang Key Laboratory of Crop Germplasm Innovation and Utilization, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Zhiyuan Zhang
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Zhenzhou Road, Yazhou District, Sanya, Hainan, 572025, China
| | - Ting Zhao
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Zhenzhou Road, Yazhou District, Sanya, Hainan, 572025, China; Zhejiang Key Laboratory of Crop Germplasm Innovation and Utilization, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Shiwei Geng
- Xinjiang Cotton Technology Innovation Center/Xinjiang Key Laboratory of Cotton Genetic Improvement and Intelligent Production/National Cotton Engineering Technology Research Center, Cotton Research Institute of Xinjiang Uyghur Autonomous Region Academy of Agricultural Sciences, Wulumuqi, 830091, Xinjiang, China
| | - Xueying Guan
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Zhenzhou Road, Yazhou District, Sanya, Hainan, 572025, China; Zhejiang Key Laboratory of Crop Germplasm Innovation and Utilization, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
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36
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Song R, Lv B, He Z, Li H, Wang H. Rhizosphere metabolite dynamics in continuous cropping of vineyards: Impact on microflora diversity and co-occurrence networks. Microbiol Res 2025; 296:128134. [PMID: 40068342 DOI: 10.1016/j.micres.2025.128134] [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: 10/21/2024] [Revised: 02/09/2025] [Accepted: 03/01/2025] [Indexed: 04/10/2025]
Abstract
The metabolism of the crop rhizosphere affects microflora diversity and nutrient cycling. However, understanding rhizosphere metabolism in suitable crops within arid desert environments and its impact on microflora interactions remains limited. Through metagenomic and non-targeted metabolomic sequencing of rhizosphere soils from one uncultivated land and four vineyards with cropping years of 5, 10, 15 and 20 years, the critical importance of rhizosphere metabolites in maintaining bacterial and fungal diversity was elucidated. The results revealed that Nocardioides, Streptomyces, and Solirubrobacter were the relatively abundant bacterial genera in rhizosphere soils, while Rhizophagus, Glomus, and Pseudogymnoascus were the relatively abundant fungal genera. The composition of rhizosphere metabolic changed significantly during the continuous cropping of grapevines. Dimethylglycine, Formononetin, and Dehydroepiandrosterone were the most important metabolites. Enrichment analysis revealed significant involvement of metabolic pathways such as biosynthesis of amino acids, unsaturated fatty acids, and linoleic acid metabolism. Procrustes analysis highlighted stronger correlations between rhizosphere metabolites and bacterial community compared to those of fungal community. This suggests distinct responses of microflora to crop-released chemical elements across different soil habitats. Co-occurrence network analysis demonstrated complex associations between rhizosphere metabolites and soil microflora, the positive correlations between rhizosphere metabolites and microflora networks predominated over negative correlations. Partial least squares path model indicated that the effect of cropping years on rhizosphere metabolites was greater than that on bacterial microflora diversity. Futhermore, pH, total phosphorus, and alkali-hydrolyzed nitrogen were the key environmental factors affecting rhizosphere metabolites and microbial diversity. These results deepen our valuable insights into the complex biological processes that rhizosphere metabolites influence on microorganisms, and provide strong support for maintaining microbial diversity in farmland soils in arid regions.
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Affiliation(s)
- Rui Song
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Bihan Lv
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Zhouyang He
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Hua Li
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China; Shanxi Engineering Research Center for Viti-Viniculture, Yangling, Shanxi 712100, China.
| | - Hua Wang
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China; Shanxi Engineering Research Center for Viti-Viniculture, Yangling, Shanxi 712100, China.
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Wang R, Li X, Wang C, Shi Y, Xiong D, Huang D, Wang Z, Ye L. Tight orchestration of wound healing phase through metal-organic compounds. Biomaterials 2025; 318:123160. [PMID: 39914195 DOI: 10.1016/j.biomaterials.2025.123160] [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: 08/26/2024] [Revised: 01/08/2025] [Accepted: 01/28/2025] [Indexed: 03/05/2025]
Abstract
Cutaneous wound healing remains a common health problem. Metal-organic frameworks (MOFs) have emerged as an advanced therapeutic platform for promoted wound healing. However, there is a lack of MOF particles possessing excellent stability, biocompatibility, and reactive oxygen species (ROS) scavenging ability for tight orchestration of wound healing. Herein, we synthetize therapeutic MOF particles named PgC3Zn and employ them as skin sprays for wound repair. At the inflammatory stage, the pH- and ROS-responsive Zn2+ release of PgC3Zn alleviates oxidative stress and exerts antibacterial and anti-inflammatory efficacy. During the proliferation stage, PgC3Zn promote the migration and proliferation of fibroblasts, the re-epithelialization of keratinocytes, and the angiogenesis of endothelial cells. During the remodeling stage, PgC3Zn effectively facilitate the wound closure and collagen deposition. Moreover, multiple endogenous growth factors have been identified to contribute to the wound healing process. Importantly, PgC3Zn exhibit excellent biocompatibility and remarkably accelerate the healing process in both acute and infected rat full-thickness skin wound models in vivo. Consistently, transcriptomic data illustrate the multi-stage and multi-functional regulation effects of PgC3Zn in promoting wound healing. This study proposes versatile and biocompatible PgC3Zn MOF particles with potentials for enhancing the management of acute and infected skin wounds.
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Affiliation(s)
- Rui Wang
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China; Department of Cariology and Endodontics, West China School of Stomatology, Sichuan University, Chengdu, China.
| | - Xin Li
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Chenglin Wang
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China; Department of Cariology and Endodontics, West China School of Stomatology, Sichuan University, Chengdu, China
| | - Yu Shi
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Ding Xiong
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Dingming Huang
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China; Department of Cariology and Endodontics, West China School of Stomatology, Sichuan University, Chengdu, China.
| | - Zhenming Wang
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China; Department of Cariology and Endodontics, West China School of Stomatology, Sichuan University, Chengdu, China.
| | - Ling Ye
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China; Department of Cariology and Endodontics, West China School of Stomatology, Sichuan University, Chengdu, China
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38
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Fang F, Gong Z, Guo C, Wang C, Ding L, Zhou B, Chen S. Establishment of an ovarian cell line from tomato grouper (Cephalopholis sonnerati) and its transcriptome response to ISKNV infection. FISH & SHELLFISH IMMUNOLOGY 2025; 162:110304. [PMID: 40185294 DOI: 10.1016/j.fsi.2025.110304] [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: 01/22/2025] [Revised: 03/27/2025] [Accepted: 03/30/2025] [Indexed: 04/07/2025]
Abstract
Tomato grouper (Cephalopholis sonnerati) is an economically efficient and nutritious species, whose expansion through factory farming in recent years has been hindered by the frequent occurrence of diseases, limiting the development of its aquaculture industry. The establishment of reliable cell lines is fundamental for conducting comprehensive immunological and virological research on the tomato grouper. In this study, we established an ovarian cell line from tomato grouper, designated TGGO. The TGGO cells were passaged for over 70 passages and cultured in L-15 medium supplemented with 15 % FBS at 27 °C, exhibiting a fibroblast-like morphology. It was determined that the TGGO cells were derived from the tomato grouper through mitochondrial coI gene sequencing. Karyotype analysis determined a chromosome number of 2n = 48. The survival rate of cells cryopreserved in liquid nitrogen for 5 months exceeded 70 % upon thawing. The cells were transfected with the EGFP-N3 plasmid and Cy3-labeled scrambled siRNA, and clear green and red fluorescence were observed. Additionally, the cells exhibited sensitivity to ISKNV, displaying a clear cytopathic effect (CPE) at 24 h post-infection, with viral particles observed under transmission electron microscopy. Transcriptomic analysis of ISKNV-infected TGGO cells showed significant enrichment of differentially expressed genes in pathways related to viral infection, nucleic acid replication, and immune response. Notable pathways include ECM-receptor interaction, PI3K-Akt signaling, viral protein interaction with cytokines and cytokine receptors, ribosome biogenesis, and DNA replication. These findings suggest that the TGGO cell line is susceptible to ISKNV infection and can be used to study this virus. Therefore, the TGGO cell line is anticipated to become a valuable resource for in vitro research on virology and other biological processes in tomato grouper.
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Affiliation(s)
- Fei Fang
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China; State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
| | - Zhihong Gong
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
| | - Chenfei Guo
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
| | - Chongwei Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
| | - Lanqing Ding
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
| | - Bo Zhou
- Wanning Linlan Aquaculture Co., Ltd, Wanning, Hainan, 571528, China
| | - Songlin Chen
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China; Yazhoubay Agriculture and Aquaculture Development Co., Ltd, Sanya, Hainan, 572025, China.
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Zheng J, Hu J, Guo R, Lu D, Dai X, Wang R, Jin H, Sun Z, Li J, Chen F, Chen J, Wang P. Early warning on the potential harmful algal bloom species in Beibu Gulf of South China Sea under the background of climate change and human activity. ENVIRONMENTAL RESEARCH 2025; 276:121516. [PMID: 40180263 DOI: 10.1016/j.envres.2025.121516] [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: 11/10/2024] [Revised: 03/12/2025] [Accepted: 03/30/2025] [Indexed: 04/05/2025]
Abstract
Human activity and global climate change increasingly affect marine environments, leading to increases in harmful algal blooms (HABs) caused by phytoplankton. These blooms pose significant threats to public health, tourism, fisheries, and ecosystems. As an important fishing ground and tourist destination, the Beibu Gulf faces growing environmental pressure. This study sought to assess the phytoplankton community structure and status of HABs, with a focus on potential HAB species. Using environmental DNA (eDNA) metabarcoding, summer and winter surveys at both coastal and offshore waters revealed 66 potential HAB species, 23 of which were newly recorded in the Beibu Gulf. The potential HAB species exhibited greater richness and relative abundance in summer than in winter. Offshore areas showed greater diversity, whereas coastal areas showed greater relative abundance. Temperature emerged as the most influential factor shaping phytoplankton composition, and pH was found to play an important role in coastal areas. Nutrients such as silicate and ammonium are critical for the distribution of potential HAB species. Among the potential HAB species, Cyclotella cryptica predominated in coastal areas during winter, whereas Chaetoceros tenuissimus predominated in summer. Some species that caused severe HAB events in other oceanic regions were first detected in this study, including Margalefidinium polykrikoides, Karlodinium veneficum, and Prorocentrum concavum. This study revealed the diversity and complexity of the phytoplankton community in the Beibu Gulf, emphasizing the critical importance of monitoring and early warning of potential HAB species, particularly those driven by human activities and climate change.
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Affiliation(s)
- Junjie Zheng
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, China
| | - Jiarong Hu
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, China; School of Marine Sciences, Sun Yat-sen University, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519082, China
| | - Ruoyu Guo
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, China
| | - Douding Lu
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, China
| | - Xinfeng Dai
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, China
| | - Ruifang Wang
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, China; Ocean College, Zhejiang University, Zhoushan, 316021, China
| | - Haiyan Jin
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, China
| | - Zihan Sun
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, China
| | - Jiongyi Li
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, China; School of Mathematics, Hangzhou Normal University, Hangzhou, 311121, China
| | - Fajin Chen
- College of Ocean and Meteorology, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Jianfang Chen
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, China
| | - Pengbin Wang
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, China; Ocean College, Zhejiang University, Zhoushan, 316021, China.
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Jing R, Wu P, Wang P, Zhao X, Baz NM, Wang J, Dong L, Han Y, Chen H, Cao H. The activity annotation of peach glycosyltransferase PpUGT78B based on engineering bacterial anthocyanin biosynthesis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2025; 224:109913. [PMID: 40239249 DOI: 10.1016/j.plaphy.2025.109913] [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: 01/26/2025] [Revised: 04/07/2025] [Accepted: 04/09/2025] [Indexed: 04/18/2025]
Abstract
Glycosylation modification allows the formation of anthocyanin from anthocyanidin, which enhances the stability of anthocyanins and improves fruit coloration and anthocyanin availability as a human functional component. Flavonoid glycosyltransferases (UFGT) are responsible for catalyzing anthocyanidin glycosylation. In the present study, to better clarify peach (Prunus persica L.) UFGT (PpUGT78B) function, an engineering bacterial system was constructed, which used the anthocyanidin synthase (ANS) gene for producing cyanidin with the incorporation of (+)-catechin precursors and further synthesized cyanidin-3-O-glucoside (C3G) with UFGT co-expression. In addition, it was found that expression of fusion proteins with ANS and UFGT could improve C3G production by about 15 %-20 % in engineering bacterial systems. Furthermore, combining the molecular modeling prediction and targeted mutagenesis, this engineering bacterial system linked some residues in PpUGT78B to glycosylation capacity, which involved F210, L148, Q393, G391, and H230, whose mutation resulted in reduced enzyme activity or even loss and also involved F203 and S29 whose mutation resulted in the increased catalytic activity. Subsequently, a natural mutation of PpUGT78B was detected by analyzing 109 peach genome re-sequencing data, and two residue mutants (E82D, V276F) were found in two peach varieties. Further, these two natural mutation sites were confirmed to reduce PpUGT78B activity in engineering bacterial systems. This study demonstrates the effectiveness of the engineering bacteria system in anthocyanin biosynthesis. It offers valuable insights into the functional and structural roles of PpUGT78B, advancing our understanding of anthocyanin glycosylation.
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Affiliation(s)
- Ruyu Jing
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071000, China; Baotou Agricultural and Animal Husbandry Science Research Institute, Baotou, Inner Mongolia, 014010, China
| | - Pengyu Wu
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071000, China
| | - Pengfei Wang
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071000, China
| | - Xulei Zhao
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071000, China
| | - Naila Mir Baz
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071000, China
| | - Jiahui Wang
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071000, China
| | - Lemeng Dong
- Plant Hormone Biology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, Netherlands
| | - Yan Han
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071000, China
| | - Haijiang Chen
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071000, China
| | - Hongbo Cao
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071000, China.
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Zhang H, Pan Y, Wang M, Wang J, Huang J, Ma R, Yang S, Ma W, Yu S, Cui Y. SETD2 regulates oocytes in vitro maturation through histone methylation and maternal mRNA degradation in yak. Theriogenology 2025; 240:117387. [PMID: 40120144 DOI: 10.1016/j.theriogenology.2025.117387] [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: 12/09/2024] [Revised: 02/26/2025] [Accepted: 03/10/2025] [Indexed: 03/25/2025]
Abstract
In vitro maturation (IVM) of oocytes is a vital aspect of assisted reproductive technology (ART), and its proper application can enhance reproductive efficiency. However, owing to the scarcity of research on the IVM of yak oocytes, its application in yak breeding remains underexplored. Therefore, in this study, we conducted high-throughput mRNA sequencing of immature and mature yak oocytes, which revealed transcriptomic changes during the IVM process in this unique high-altitude domesticated animal. Transcriptomic analysis also identified the histone methyltransferase SET domain-containing 2 (SETD2) as a key factor associated with post-translational modifications during oocyte maturation. To determine the role of SETD2 in oocytes, we employed the SETD2 inhibitor EZM0414 during oocyte maturation. Inhibition of SETD2 resulted in a significant reduction in histone methylation levels, lower oocyte maturation rate in vitro, and suppression of maternal mRNAs degradation suppression (P < 0.05). These findings indicated that SETD2 modulates oocyte maturation by regulating histone methylation and maternal mRNAs degradation. Furthermore, suppression of SETD2 markedly reduced the expression of oocyte secretion-related proteins (TSG6 and GDF9) and cumulus expansion-related protein (PTGS2), demonstrating that oocyte secretion and cumulus expansion were positively correlated with SETD2. Overall, our findings establish SETD2 as an essential regulator of yak oocyte maturation via histone methylation and maternal mRNAs degradation.
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Affiliation(s)
- Hui Zhang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, China; Gansu Provincial Livestock Embryo Engineering Technology Innovation Center, Lanzhou, 730070, China
| | - Yangyang Pan
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, China; Gansu Provincial Livestock Embryo Engineering Technology Innovation Center, Lanzhou, 730070, China
| | - Meng Wang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, China; Gansu Provincial Livestock Embryo Engineering Technology Innovation Center, Lanzhou, 730070, China
| | - Jinglei Wang
- Gansu Provincial Livestock Embryo Engineering Technology Innovation Center, Lanzhou, 730070, China
| | - Jiaxin Huang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, China
| | - Rui Ma
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, China; Gansu Provincial Livestock Embryo Engineering Technology Innovation Center, Lanzhou, 730070, China
| | - Shanshan Yang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, China; Gansu Provincial Livestock Embryo Engineering Technology Innovation Center, Lanzhou, 730070, China
| | - Wenbin Ma
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, China; Gansu Provincial Livestock Embryo Engineering Technology Innovation Center, Lanzhou, 730070, China
| | - Sijiu Yu
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, China; Gansu Provincial Livestock Embryo Engineering Technology Innovation Center, Lanzhou, 730070, China.
| | - Yan Cui
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, China; Gansu Provincial Livestock Embryo Engineering Technology Innovation Center, Lanzhou, 730070, China.
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Lian CY, Yao XY, Lv ZH, Zhang XL, Shao JW. Genetic diversity of canine coronavirus identified in dogs in yulin city, southern China. Virology 2025; 608:110528. [PMID: 40233446 DOI: 10.1016/j.virol.2025.110528] [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: 09/29/2024] [Revised: 03/27/2025] [Accepted: 04/07/2025] [Indexed: 04/17/2025]
Abstract
The global outbreak of the novel coronavirus has renewed interest in related viral pathogens, including canine coronavirus (CCoV), which causes severe gastroenteritis, diarrhea, and vomiting in dogs worldwide. While cases of CCoV have been reported in China, specific instances in the Guangxi Zhuang Autonomous Region-a major center for dog breeding and consumption-have not been documented. In this study, we collected spleen tissue samples from dogs in Yulin city and conducted meta-transcriptomic sequencing. Bioinformatics analysis confirmed CCoV presence in these samples. Furthermore, virus screening and phylogenetic analyses identified the circulation of two CCoV genotypes within the dog population, revealing an overall prevalence of 14.2 %, with CCoV-IIb being the predominant genotype. Notably, two significant recombination events were detected among the analyzed strains. These findings provide valuable insights into the presence and genetic diversity of CCoV Yulin's dog populations, enhancing the understanding of its genetic variation and evolution.
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Affiliation(s)
- Chun-Yang Lian
- School of Animal Science and Technology, Foshan University, Foshan 528225, China
| | - Xin-Yan Yao
- School of Animal Science and Technology, Foshan University, Foshan 528225, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Zhi-Hang Lv
- School of Animal Science and Technology, Foshan University, Foshan 528225, China
| | - Xue-Lian Zhang
- School of Animal Science and Technology, Foshan University, Foshan 528225, China
| | - Jian-Wei Shao
- School of Animal Science and Technology, Foshan University, Foshan 528225, China.
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Thilén L, Lachenaud O, Thureborn O, Razafimandimbison SG, Rydin C. Phylogeny of Palicoureeae (Rubiaceae) based on 353 low-copy nuclear genes - with particular focus on Hymenocoleus Robbr. Mol Phylogenet Evol 2025; 208:108338. [PMID: 40158785 DOI: 10.1016/j.ympev.2025.108338] [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: 01/13/2025] [Revised: 03/18/2025] [Accepted: 03/20/2025] [Indexed: 04/02/2025]
Abstract
Members of the tribe Palicoureeae of the coffee family (Rubiaceae) have a complex taxonomic history and have been the focus of few modern systematic studies. The tribe comprises about 1,100 tropical species in ten genera. To investigate phylogeny, we used a target capture approach and the angiosperm-wide Angiosperms353 bait set to produce genomic data for a representative taxon sample of Palicoureeae, with particular focus on the African genus Hymenocoleus. Using coalescent-based inference methods, we find that Puffia gerrardii (recently separated from Geophila) is sister to Hymenocoleus. The deepest split in Hymenocoleus is highly affected by incomplete lineage sorting, possibly as a consequence of rapid speciation during the early evolution of the clade. Remaining interspecific relationships in Hymenocoleus could be confidently resolved and while Robbrecht's traditional infrageneric classification scheme based on floral features is not supported as reflecting evolution in the group, we find that several other features do, e.g. characters of pyrenes and involucral cups. Although not free of challenges, a strong advantage with our analytical approach is that gene tree heterogeneity can be taken into account. Including flanking regions yielded data sets that had the strongest power to reject polytomies and produced less gene tree error, resulting in species trees with higher normalised quartet scores and higher average support compared to trees inferred only from exon data. Presumably paralogous loci are often filtered out prior to species tree estimation but we find that they may contribute important phylogenetic information when using an inference method that actively accounts for them.
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Affiliation(s)
- Lovisa Thilén
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden.
| | - Olivier Lachenaud
- Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, Belgium; Herbarium et Bibliothèque de Botanique Africaine, CP 265, Université Libre de Bruxelles, Boulevard du Triomphe, 1050 Brussels, Belgium
| | - Olle Thureborn
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
| | | | - Catarina Rydin
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
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Luo W, Yi X, Zhang X, Yuan C, Wei W, Li X, Pu D, Yang J, Zheng H. Taxonomic reassessment of genomes from a divergent population of Streptococcus suis by average nucleotide identity analysis. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2025; 131:105753. [PMID: 40287079 DOI: 10.1016/j.meegid.2025.105753] [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: 01/18/2025] [Revised: 04/22/2025] [Accepted: 04/23/2025] [Indexed: 04/29/2025]
Abstract
Streptococcus spp., including the emerging zoonotic pathogen S. suis, represent a dominant bacterial population in the porcine nasopharynx. Species identification within the Streptococcus genus remains challenging and frequently ambiguous, resulting in indistinct species boundaries. By employing comparative genomic analyses, a previous study categorized S. suis into a central population and divergent lineages, based on the single nucleotide polymorphisms (SNPs) within core genes and the presence or absence of accessory genes, indicating evolutionary divergence. The divergent lineages were designated as the "out population" in this study for clarity. The 16S rRNA gene sequences of seven putative novel Streptococcus strains isolated from the throats of healthy pigs in China exhibited 100 % similarity to that of the 684_17B strain of S. suis, which clustered in the out population. This study established a threshold average nucleotide identity (ANI) value of 93.17 % for the identification of authentic S. suis. All the 645 genomes from the out population fell below this threshold, indicating that they did not belong to S. suis. Further taxonomic assessment of the 645 genomes from the out population revealed 18 clusters based on pairwise ANI comparisons, using a 92.33 % threshold, determined by pairwise ANI comparisons among the 2422 genomes from the central population of S. suis. These clusters were identified as 12 novel Streptococcus spp. (Streptococcus sp. nov-1-12) and six known Streptococcus spp. by ANI comparisons with type or reference genomes of 98 known Streptococcus spp. The study provides a useful framework for the identification of authentic S. suis and the determination of Streptococcus sp. nov.
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Affiliation(s)
- Wenbo Luo
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xueli Yi
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Guangxi, 533000, China
| | - Xiyan Zhang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | | | - Wenfei Wei
- Baise Center for Animal Disease Prevention and Control, Baise, China
| | - Xuezhen Li
- Baise Center for Animal Disease Prevention and Control, Baise, China
| | - Danna Pu
- Research Institute of Public Health, School of Medicine, Nankai University, Tianjin, China
| | - Jing Yang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Han Zheng
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China; MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, School of Public Health, Shanxi Medical University, Taiyuan, China.
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Liang T, Jiang T, Liang Z, Li L, Chen Y, Chen T, Yang L, Zhang N, Dong B, Xie X, Gu B, Wu Q. Gut microbiota-driven BCAA biosynthesis via Staphylococcus aureus -expressed acetolactate synthase impairs glycemic control in type 2 diabetes in South China. Microbiol Res 2025; 296:128145. [PMID: 40138872 DOI: 10.1016/j.micres.2025.128145] [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: 06/29/2024] [Revised: 03/12/2025] [Accepted: 03/14/2025] [Indexed: 03/29/2025]
Abstract
An increase in branched-chain amino acid (BCAA) levels can result in insulin resistance at different stages of type 2 diabetes (T2D), however, the causes of this increase are unclear. We performed metagenomics and metabolomics profiling in patients with prediabetes (PDM), newly diagnosed diabetes (NDDM), and post-medication type 2 diabetes (P2DM) to investigate whether altered gut microbes and metabolites could explain the specific clinical characteristics of different disease stages of T2D. Here we identify acetolactate synthase (ALS) a BCAA biosynthesis enzyme in Staphylococcus aureus as a cause of T2D insulin resistance. Compared with healthy peoples, patients with PDM, NDDM, and P2DM groups, especially in P2DM group, have increased faecal numbers of S. aureus. We also demonstrated that insulin administration may be a risk factor for S. aureus infection in T2D. The presence of ALS-positive S. aureus correlated with the levels of BCAAs and was associated with an increased fasting blood glucose (FBG) and insulin resistance. Humanized microbiota transplantation experiment indicated that ALS contributes to disordered insulin resistance mediated by S. aureus. We also found that S. aureus phage can reduced the FBG levels and insulin resistance in db/db mice. The ALS-positive S. aureus are associated with insulin resistance in T2D, opening a new therapeutic avenue for the prevention or treatment of diabetes.
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Affiliation(s)
- Tingting Liang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China; Department of Clinical Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China.
| | - Tong Jiang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Zhuang Liang
- Department of Rehabilitation Hospital Pain Ward, Xi'an Jiaotong University Affiliated Honghui Hospital, Xi'an, Shaanxi 710054, China
| | - Longyan Li
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Ya Chen
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Tong Chen
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Lingshuang Yang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Ni Zhang
- Department of Clinical Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Bo Dong
- Department of Rehabilitation Hospital Pain Ward, Xi'an Jiaotong University Affiliated Honghui Hospital, Xi'an, Shaanxi 710054, China.
| | - Xinqiang Xie
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China.
| | - Bing Gu
- Department of Clinical Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China.
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China.
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Liu M, Wang S, Zhou H, Liu H, Huang D, Liu L, Li Q, Chen H, Lei Y, Jin LN, Zhang W. Thermal environment driving specific microbial species to form the visible biofilms on the UNESCO World Heritage Dazu Rock Carvings. ENVIRONMENTAL RESEARCH 2025; 276:121510. [PMID: 40174744 DOI: 10.1016/j.envres.2025.121510] [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: 01/03/2025] [Revised: 03/28/2025] [Accepted: 03/29/2025] [Indexed: 04/04/2025]
Abstract
The Dazu Rock Carvings, a UNESCO World Heritage site with over a millennium of history, are facing significant deterioration from microbial biofilms. However, the key microbial species responsible and the environmental factors driving their growth remain unclear. To address this gap, we conducted metagenomic sequencing to characterize the microbial community on the carvings, followed by correlation analyses with a variety of environmental factors in the surrounding air and within the rocks. Bacterial communities exhibited significantly higher richness and diversity than eukaryotic communities, though diversity metrics showed no significant differences between visibly colonized and uncolonized surfaces. We identified a distinctive consortium of 64 bacterial species, 35 fungal species, and 1 algal species specifically associated with visible biofilms, occurring at 9.56-fold higher relative abundance in colonized areas. These microorganisms contribute to characteristic green, brown-black, and white coloration on the carvings. Statistical analysis revealed absolute humidity and dew point temperature as key environmental factors influencing biofilm visibility, with thresholds of 21.00 g/m3 and 23.4 °C respectively, above which biofilms became visible. This study provides precise targets for conservation efforts and establishes critical environmental parameters to guide preservation strategies for this irreplaceable cultural heritage.
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Affiliation(s)
- Meng Liu
- School of Civil Engineering, Chongqing University, Chongqing, 400045, China; Joint International Research Laboratory of Green Buildings and Built Environments (Ministry of Education), Chongqing University, Chongqing, 400045, China; National Centre for International Research of Low-carbon and Green Buildings, Chongqing University, Chongqing, 400045, China
| | - Shuwan Wang
- School of Civil Engineering, Chongqing University, Chongqing, 400045, China; Joint International Research Laboratory of Green Buildings and Built Environments (Ministry of Education), Chongqing University, Chongqing, 400045, China; National Centre for International Research of Low-carbon and Green Buildings, Chongqing University, Chongqing, 400045, China
| | - Hua Zhou
- School of Civil Engineering, Chongqing University, Chongqing, 400045, China; Joint International Research Laboratory of Green Buildings and Built Environments (Ministry of Education), Chongqing University, Chongqing, 400045, China; National Centre for International Research of Low-carbon and Green Buildings, Chongqing University, Chongqing, 400045, China
| | - Huan Liu
- School of Civil Engineering, Chongqing University, Chongqing, 400045, China; Joint International Research Laboratory of Green Buildings and Built Environments (Ministry of Education), Chongqing University, Chongqing, 400045, China; National Centre for International Research of Low-carbon and Green Buildings, Chongqing University, Chongqing, 400045, China.
| | - Di Huang
- School of Civil Engineering, Chongqing University, Chongqing, 400045, China; Joint International Research Laboratory of Green Buildings and Built Environments (Ministry of Education), Chongqing University, Chongqing, 400045, China; National Centre for International Research of Low-carbon and Green Buildings, Chongqing University, Chongqing, 400045, China
| | - Lumeng Liu
- School of Civil Engineering, Chongqing University, Chongqing, 400045, China; Joint International Research Laboratory of Green Buildings and Built Environments (Ministry of Education), Chongqing University, Chongqing, 400045, China; National Centre for International Research of Low-carbon and Green Buildings, Chongqing University, Chongqing, 400045, China
| | - Qisheng Li
- School of Civil Engineering, Chongqing University, Chongqing, 400045, China; Joint International Research Laboratory of Green Buildings and Built Environments (Ministry of Education), Chongqing University, Chongqing, 400045, China; National Centre for International Research of Low-carbon and Green Buildings, Chongqing University, Chongqing, 400045, China
| | - Huili Chen
- Academy of Dazu Rock Carvings, Chongqing, 402360, China
| | - Yu Lei
- Academy of Dazu Rock Carvings, Chongqing, 402360, China
| | - Ling N Jin
- Department of Civil and Environmental Engineering & Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region of China; State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong Special Administrative Region of China
| | - Wengang Zhang
- School of Civil Engineering, Chongqing University, Chongqing, 400045, China
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Ribas-Latre A, Hoffmann A, Gebhardt C, Weiner J, Arndt L, Raulien N, Gericke M, Ghosh A, Krause K, Klöting N, Pfluger PT, Sheikh BN, Ebert T, Tönjes A, Stumvoll M, Wolfrum C, Blüher M, Wagner U, Vendrell J, Fernández-Veledo S, Heiker JT. The serine protease KLK7 promotes immune cell infiltration in visceral adipose tissue in obesity. Metabolism 2025; 168:156239. [PMID: 40154838 DOI: 10.1016/j.metabol.2025.156239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2024] [Revised: 02/05/2025] [Accepted: 03/22/2025] [Indexed: 04/01/2025]
Abstract
Obesity is a major health problem associated with global metabolic dysfunction and increased inflammation. It is thus critical to identify the mechanisms underlying the crosstalk between immune cells and adipose tissue that drive cardiovascular and metabolic dysfunction in obesity. Expression of the kallikrein-related serine protease 7 (KLK7) in adipose tissue is linked to inflammation and insulin resistance in high fat diet (HFD)-fed mice. Here, we engineered mice with a macrophage-specific KLK7 knockout (KLK7MKO) to investigate how KLK7 loss impacts immune cell function and obesity-related pathology. Compared to control mice, we observed lower levels of systemic inflammation, with less infiltration and activation of inflammatory macrophages in HFD-fed KLK7MKO mice, particularly in the epididymal adipose tissue. Mechanistically, we uncover that Klk7 deficiency reduces pro-inflammatory gene expression in macrophages and restricts their migration through higher cell adhesion, hallmark features of macrophages in obese conditions. Importantly, through analyses of 1143 human visceral adipose tissue samples, we uncover that KLK7 expression is associated with pathways controlling cellular migration and inflammatory gene expression. In addition, serum KLK7 levels were strongly correlated with circulating inflammatory markers in a second cohort of 60 patients with obesity and diabetes. Our work uncovers the pro-inflammatory role of KLK7 in controlling inflammatory macrophage polarization and infiltration in visceral obesity, thereby contributing to metabolic disease. Thus, targeting KLK7 to control immune cell activation may dissociate adipose dysfunction from obesity, thereby representing an alternative obesity therapy.
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Affiliation(s)
- Aleix Ribas-Latre
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany; Hospital Universitari Joan XXIII de Tarragona, Institut d'Investigació Sanitària Pere Virgili (IISPV), 43005 Tarragona, Spain; CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM)-Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Anne Hoffmann
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| | - Claudia Gebhardt
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| | - Juliane Weiner
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Lilli Arndt
- Institute of Anatomy, Leipzig University, Leipzig, Germany
| | - Nora Raulien
- Institute of Anatomy, Leipzig University, Leipzig, Germany
| | - Martin Gericke
- Institute of Anatomy, Leipzig University, Leipzig, Germany
| | - Adhideb Ghosh
- Laboratory of Translational Nutrition Biology, Institute of Food, Nutrition and Health, ETH Zürich, Schwerzenbach, Switzerland
| | - Kerstin Krause
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany; German Center for Diabetes Research, Neuherberg, Germany
| | - Nora Klöting
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| | - Paul T Pfluger
- German Center for Diabetes Research, Neuherberg, Germany; Research Unit NeuroBiology of Diabetes, Institute for Diabetes and Obesity, Helmholtz Centre, Munich, Germany; Division of Neurobiology of Diabetes, TUM School of Medicine & Health, Technical University of Munich, Munich, Germany
| | - Bilal N Sheikh
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany; Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Thomas Ebert
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Anke Tönjes
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Michael Stumvoll
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany; Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany; German Center for Diabetes Research, Neuherberg, Germany
| | - Christian Wolfrum
- Laboratory of Translational Nutrition Biology, Institute of Food, Nutrition and Health, ETH Zürich, Schwerzenbach, Switzerland
| | - Matthias Blüher
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany; Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany; German Center for Diabetes Research, Neuherberg, Germany
| | - Ulf Wagner
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Joan Vendrell
- Hospital Universitari Joan XXIII de Tarragona, Institut d'Investigació Sanitària Pere Virgili (IISPV), 43005 Tarragona, Spain; CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM)-Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain; Universitat Rovira i Virgili (URV), 43201 Reus, Spain
| | - Sonia Fernández-Veledo
- Hospital Universitari Joan XXIII de Tarragona, Institut d'Investigació Sanitària Pere Virgili (IISPV), 43005 Tarragona, Spain; CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM)-Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain; Universitat Rovira i Virgili (URV), 43201 Reus, Spain
| | - John T Heiker
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany; Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany; Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Leipzig, Germany.
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48
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Wang Q, Li S, Wei Y, Xu C, Liu X, Wang X, Chai W, Mou W, Chen X, Li C, Wang C, Gui J. An increase in IL-10-producing DNT cells is associated with the pathogenesis of pediatric SLE. Clin Immunol 2025; 276:110490. [PMID: 40158789 DOI: 10.1016/j.clim.2025.110490] [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: 01/18/2025] [Revised: 03/20/2025] [Accepted: 03/25/2025] [Indexed: 04/02/2025]
Abstract
Systemic lupus erythematosus (SLE) is a chronic autoimmune disease that causes immune system overactivity and organ damage. Among T-cell subsets involved in SLE, CD4 and CD8 double-negative αβT (DNT) cells have attracted attention in recent years, although their role in SLE remains poorly understood. Examining the minute intricacies, particularly signaling pathway modifications is crucial, as it may unveil potential therapeutic targets and lead to the development of more effective treatments. Our study found increased DNT cells in pediatric SLE patients, with elevated IL-10 signaling. These IL-10-producing DNT cells were positively related to disease activity defined by SLE Disease Activity Index (SLEDAI), and were further elevated in patients with lupus nephritis. Additionally, our results indicated that IL-10-producing DNT cells correlated positively with anti-Sm autoantibodies. Collectively, our study revealed that modulation of IL-10 production within DNT-cell subset could affect both immune regulation and autoantibody production, contributing to the immunological dysregulation in SLE.
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Affiliation(s)
- Qixin Wang
- Laboratory of Tumor Immunology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China; Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Shipeng Li
- Department of Rheumatology, National Centre for Children's Health, Beijing Children's Hospital, Capital Medical University, No. 56 Nan Li Shi Lu, Beijing 100045, China
| | - Yannan Wei
- Inner Mongolia Xilingol League Central Hospital, Xilinhaote 026000, China
| | - Chen Xu
- Inner Mongolia Xilingol League Central Hospital, Xilinhaote 026000, China
| | - Xiangjun Liu
- Laboratory of Tumor Immunology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China; Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Xiaolin Wang
- Laboratory of Tumor Immunology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China; Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Wenjia Chai
- Laboratory of Tumor Immunology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China; Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Wenjun Mou
- Laboratory of Tumor Immunology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China; Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Xi Chen
- Laboratory of Tumor Immunology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China; Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Caifeng Li
- Department of Rheumatology, National Centre for Children's Health, Beijing Children's Hospital, Capital Medical University, No. 56 Nan Li Shi Lu, Beijing 100045, China.
| | - Caisheng Wang
- Inner Mongolia Xilingol League Central Hospital, Xilinhaote 026000, China.
| | - Jingang Gui
- Laboratory of Tumor Immunology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China; Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China.
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49
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Ren H, Liu S, Ji D, Li X, Sun X, Wang W, Liu T, Li Y. Transcriptome analysis reveals the potential role of neural factor EN1 for long-terms survival in estrogen receptor-independent breast cancer. MOLECULAR THERAPY. ONCOLOGY 2025; 33:200965. [PMID: 40207200 PMCID: PMC11981748 DOI: 10.1016/j.omton.2025.200965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2024] [Revised: 01/27/2025] [Accepted: 03/05/2025] [Indexed: 04/11/2025]
Abstract
Breast cancer patients with estrogen receptor-negative (ERneg) status, encompassing triple negative breast cancer (TNBC) and human epidermal growth factor receptor 2 positive breast cancer, are confronted with a heightened risk of drug resistance, often leading to early recurrence; the biomarkers and biological processes associated with recurrence is still unclear. In this study, we analyzed bulk RNA sequencing (RNA-seq) data from 285 cancer and paracancerous samples from 155 TNBC patients, along with transcriptome data from 11 independent public cohorts comprising 7,449 breast cancer patients and 26 single-cell RNA-seq datasets. Our results revealed differential enrichment of nerve-related pathways between TNBC patients with and without 10-year recurrence-free survival. We developed an early recurrence index (ERI) using a machine learning model and constructed a nomogram that accurately predicts the 10-year survival of ERneg patients (area under the curve [AUC]Training = 0.79; AUCTest = 0.796). Further analysis linked ERI to enhanced neural function and immunosuppression. Additionally, we identified EN1, the most significant ERI gene, as a potential biomarker that may regulate the tumor microenvironment and sensitize patients to immunotherapy.
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Affiliation(s)
- He Ren
- Department of Oncological Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang Province 150000, China
| | - Shan Liu
- Department of Oncological Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang Province 150000, China
| | - Dongchen Ji
- Department of Oncological Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang Province 150000, China
| | - Xue Li
- Department of Oncological Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang Province 150000, China
| | - Xue Sun
- Department of Oncological Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang Province 150000, China
| | - Wenzheng Wang
- Department of Oncological Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang Province 150000, China
| | - Tong Liu
- Department of Oncological Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang Province 150000, China
- NHC Key Laboratory of Cell Transplantation, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province 150001, China
| | - Yingpu Li
- Department of Oncological Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang Province 150000, China
- NHC Key Laboratory of Cell Transplantation, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province 150001, China
- Genomics Research Center (Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province), College of Pharmacy, Harbin Medical University, Harbin, Heilongjiang Province 150081, China
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50
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Dong Z, He M, Lin C, Ouyang W, Liu X. Crucial role of the Pht1;4 Gene in Sb(V) tolerance and uptake in Arabidopsis thaliana. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2025; 298:118308. [PMID: 40367618 DOI: 10.1016/j.ecoenv.2025.118308] [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: 02/07/2025] [Revised: 03/19/2025] [Accepted: 05/09/2025] [Indexed: 05/16/2025]
Abstract
There has been increasing awareness of the risks of antimony (Sb) in the environment, but the process of Sb(V) absorption by plants and its effects on plants remain unclear. This study focused on four independent T-DNA insertion mutant strains of Arabidopsis thaliana and wild-type (WT) plants to investigate their tolerance, uptake, and response to Sb(V). Compared with those of the WT, the Pht1;4 knockout mutant M-P4 presented greater tolerance to Sb(V) and lower absorption levels. The roots of the M-P4 were longer and the malondialdehyde (MDA) content in the roots of M-P4 was lower than WT (0.194 < 1.333, μM/mg FW). The amount of Sb(V) absorbed by the roots of M-P4 under Sb(V) treatment was lower than that absorbed by WT plants (by 25 %-50 %), and the levels of Sb in the stems and leaves were also lower. Moreover, the transmembrane transport ratio of Sb(V) in M-P4 was lower than that in the WT (0.748 < 0.937). The Pht1;1 knockout mutant exhibited a predominant transmembrane absorption mode for Sb(V), while gene expression data show that knocking out either Pht1;1 or Pht1;4 leads to the upregulation of the other gene. These results collectively demonstrate that the characteristics of M-P4 are due to the important role of Pht1;4 in Sb(V) transport. In summary, this study investigates the influence of several genes on plant tolerance and uptake to Sb(V) and elucidates the crucial role of the Pht1;4 gene, shedding light on the development of Sb phytoremediation strategies and Sb-resistant plants.
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Affiliation(s)
- Ziyi Dong
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Mengchang He
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China.
| | - Chunye Lin
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Wei Ouyang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China; Advanced Interdisciplinary Institute of Environment and Ecology, Beijing Normal University, Zhuhai 519087, China
| | - Xitao Liu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
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