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Yang J, Qureshi M, Kolli R, Peacock TP, Sadeyen JR, Carter T, Richardson S, Daines R, Barclay WS, Brown IH, Iqbal M. The haemagglutinin gene of bovine-origin H5N1 influenza viruses currently retains receptor-binding and pH-fusion characteristics of avian host phenotype. Emerg Microbes Infect 2025; 14:2451052. [PMID: 39803980 PMCID: PMC11776067 DOI: 10.1080/22221751.2025.2451052] [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: 09/27/2024] [Revised: 01/01/2025] [Accepted: 01/05/2025] [Indexed: 01/29/2025]
Abstract
Clade 2.3.4.4b H5N1 high pathogenicity avian influenza virus (HPAIV) has caused a panzootic affecting all continents except Australia, expanding its host range to several mammalian species. In March 2024, H5N1 HPAIV was first detected in dairy cattle and goats in the United States. Over 891 dairy farms across 16 states have tested positive until 25 December 2024, with zoonotic infections reported among dairy workers. This raises concerns about the virus undergoing evolutionary changes in cattle that could enhance its zoonotic potential. The Influenza glycoprotein haemagglutinin (HA) facilitates entry into host cells through receptor binding and pH-induced fusion with cellular membranes. Adaptive changes in HA modulate virus-host cell interactions. This study compared the HA genes of cattle and goat H5N1 viruses with the dominant avian-origin clade 2.3.4.4b H5N1 in the United Kingdom, focusing on receptor binding, pH fusion, and thermostability. All the tested H5N1 viruses showed binding exclusively to avian-like receptors, with a pH fusion of 5.9, outside the pH range associated with efficient human airborne transmissibility (pH 5.0-5.5). We further investigated the impact of emerging HA substitutions seen in the ongoing cattle outbreaks, but saw little phenotypic difference, with continued exclusive binding to avian-like receptor analogues and pHs of fusion above 5.8. This suggests that the HA genes from the cattle and goat outbreaks do not pose an enhanced threat compared to circulating avian viruses. However, given the rapid evolution of H5 viruses, continuous monitoring and updated risk assessments remain essential to understanding virus zoonotic and pandemic risks.
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Affiliation(s)
| | | | | | - Thomas P. Peacock
- The Pirbright Institute, Pirbright, UK
- Department of Infectious Disease, Imperial College London, London, UK
| | | | | | | | | | - Wendy S. Barclay
- Department of Infectious Disease, Imperial College London, London, UK
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2
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Goel V, Ding J, Hatuwal B, Giri E, Deliberto TJ, Lowe J, Webby R, Emch M, Wan XF. Ecological drivers of evolution of swine influenza in the United States: a review. Emerg Microbes Infect 2025; 14:2455598. [PMID: 39817666 PMCID: PMC11780704 DOI: 10.1080/22221751.2025.2455598] [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] [Indexed: 01/18/2025]
Abstract
Influenza A viruses (IAVs) pose a major public health threat due to their wide host range and pandemic potential. Pigs have been proposed as "mixing vessels" for avian, swine, and human IAVs, significantly contributing to influenza ecology. In the United States, IAVs are enzootic in commercial swine farming operations, with numerous genetic and antigenic IAV variants having emerged in the past two decades. However, the dynamics of intensive swine farming systems and their interactions with ecological factors influencing IAV evolution have not been systematically analysed. This review examines the evolution of swine IAVs in commercial farms, highlighting the role of multilevel ecological factors. A total of 61 articles published after 2000 were reviewed, with most studies conducted after 2009 in Midwestern US, followed by Southeast and South-central US. The findings reveal that ecological factors at multiple spatial scales, such as regional transportation networks, interconnectedness of swine operations, farm environments, and presence of high-density, low-genetic diversity herds, can facilitate virus transmission and enhance virus evolution. Additionally, interactions at various interfaces, such as between commercial swine and feral swine, humans, or wild birds contribute to the increase in genetic diversity of swine IAVs. The review underscores the need for comprehensive studies and improved data collection to better understand the ecological dynamics influencing swine IAV evolution. This understanding is crucial for mitigating disease burden in swine production and reducing the risk of zoonotic influenza outbreaks.
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Affiliation(s)
- Varun Goel
- Department of Geography, University of South Carolina, Columbia, SC, USA
| | - Jessica Ding
- Department of Geography and Environment, University of North Carolina, Chapel Hill, NC, USA
| | - Bijaya Hatuwal
- NexGen Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA
- Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, MO, USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Emily Giri
- NexGen Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA
| | - Thomas J. Deliberto
- US Department of Agriculture Animal and Plant Health Inspection Service, Fort Collins, CO, USA
| | - James Lowe
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Richard Webby
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael Emch
- Department of Geography and Environment, University of North Carolina, Chapel Hill, NC, USA
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Xiu-Feng Wan
- NexGen Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA
- Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, MO, USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA
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3
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Xin J, Zhang H, Li Y, Dai Y, Chen X, Zou J, Wang R, Liu Z, Wang B. Effect of cold atmospheric plasma on common oral pathogenic microorganisms: a narrative review. Ann Med 2025; 57:2457518. [PMID: 39865862 PMCID: PMC11774187 DOI: 10.1080/07853890.2025.2457518] [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: 09/18/2024] [Revised: 12/12/2024] [Accepted: 12/13/2024] [Indexed: 01/28/2025] Open
Abstract
BACKGROUND The oral microbiota is a diverse and complex community that maintains a delicate balance. When this balance is disturbed, it can lead to acute and chronic infectious diseases such as dental caries and periodontitis, significantly affecting people's quality of life. Developing a new antimicrobial strategy to deal with the increasing microbial variability and resistance is important. Cold atmospheric plasma (CAP), as the fourth state of matter, has gradually become a hot topic in the field of biomedicine due to its good antibacterial, anti-inflammatory, and anti-tumor capabilities. It is expected to become a major asset in the regulation of oral microbiota. METHODS We conducted a search in PubMed, Medline, and Wiley databases, focusing on studies related to CAP and oral pathogenic microorganisms. We explored the biological effects of CAP and summarized the antimicrobial mechanisms behind it. RESULTS Numerous articles have shown that CAP has a potent antimicrobial effect against common oral pathogens, including bacteria, fungi, and viruses, primarily due to the synergy of various factors, especially reactive oxygen and nitrogen species. CONCLUSIONS CAP is effective against various oral pathogenic microorganisms, and it is anticipated to offer a new approach to treating oral infectious diseases. The future objective is to precisely adjust the parameters of CAP to ensure safety and efficacy, and subsequently develop a comprehensive CAP treatment protocol. Achieving this objective is crucial for the clinical application of CAP, and further research is necessary.
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Affiliation(s)
- Jiajun Xin
- Department of Prosthodontics, Hospital of Stomatology, Jilin University, Changchun, People’s Republic of China
- Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, Changchun, People’s Republic of China
| | - Hao Zhang
- Department of Prosthodontics, Hospital of Stomatology, Jilin University, Changchun, People’s Republic of China
- Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, Changchun, People’s Republic of China
| | - Yushen Li
- Department of Prosthodontics, Hospital of Stomatology, Jilin University, Changchun, People’s Republic of China
- Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, Changchun, People’s Republic of China
| | - Yifei Dai
- Department of Prosthodontics, Hospital of Stomatology, Jilin University, Changchun, People’s Republic of China
- Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, Changchun, People’s Republic of China
| | - Xiantao Chen
- Department of Prosthodontics, Hospital of Stomatology, Jilin University, Changchun, People’s Republic of China
- Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, Changchun, People’s Republic of China
| | - Jiatong Zou
- Department of Prosthodontics, Hospital of Stomatology, Jilin University, Changchun, People’s Republic of China
- Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, Changchun, People’s Republic of China
| | - Rui Wang
- Department of Prosthodontics, Hospital of Stomatology, Jilin University, Changchun, People’s Republic of China
- Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, Changchun, People’s Republic of China
| | - Zhihui Liu
- Department of Prosthodontics, Hospital of Stomatology, Jilin University, Changchun, People’s Republic of China
- Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, Changchun, People’s Republic of China
| | - Bowei Wang
- Department of Obstetrics and Gynecology, The Second Hospital of Jilin University, Changchun, People’s Republic of China
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4
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Simon SA, Aschmann V, Behrendt A, Hügler M, Engl LM, Pohlner M, Rolfes S, Brinkhoff T, Engelen B, Könneke M, Rodriguez-R LM, Bornemann TLV, Nuy JK, Rothe L, Stach TL, Beblo-Vranesevic K, Leuko S, Runzheimer K, Möller R, Conrady M, Huth M, Trabold T, Herkendell K, Probst AJ. Earth's most needed uncultivated aquatic prokaryotes. WATER RESEARCH 2025; 273:122928. [PMID: 39724798 DOI: 10.1016/j.watres.2024.122928] [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: 06/24/2024] [Revised: 11/29/2024] [Accepted: 12/06/2024] [Indexed: 12/28/2024]
Abstract
Aquatic ecosystems house a significant fraction of Earth's biosphere, yet most prokaryotes inhabiting these environments remain uncultivated. While recently developed genome-resolved metagenomics and single-cell genomics techniques have underscored the immense genetic breadth and metabolic potential residing in uncultivated Bacteria and Archaea, cultivation of these microorganisms is required to study their physiology via genetic systems, confirm predicted biochemical pathways, exploit biotechnological potential, and accurately appraise nutrient turnover. Over the past two decades, the limitations of culture-independent investigations highlighted the importance of cultivation in bridging this vast knowledge gap. Here, we collected more than 80 highly sought-after uncultivated lineages of aquatic Bacteria and Archaea with global ecological impact. In addition to fulfilling critical roles in global carbon, nitrogen, and sulfur cycling, many of these organisms are thought to partake in key symbiotic relationships. This review highlights the vital contributions of uncultured microbes in aquatic ecosystems, from lakes and groundwater to the surfaces and depths of the oceans and will guide current and future initiatives tasked with cultivating our planet's most elusive, yet highly consequential aquatic microflora.
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Affiliation(s)
- Sophie A Simon
- Department of Environmental Metagenomics, Research Center One Health Ruhr, University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Vera Aschmann
- Department of Water Microbiology, TZW: DVGW-Technologiezentrum Wasser, Karlsruhe, Germany
| | - Annika Behrendt
- Department of Water Microbiology, TZW: DVGW-Technologiezentrum Wasser, Karlsruhe, Germany
| | - Michael Hügler
- Department of Water Microbiology, TZW: DVGW-Technologiezentrum Wasser, Karlsruhe, Germany
| | - Lisa M Engl
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Marion Pohlner
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Sönke Rolfes
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Bert Engelen
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Martin Könneke
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Luis M Rodriguez-R
- Department of Microbiology and Digital Science Center (DiSC), University of Innsbruck, Austria
| | - Till L V Bornemann
- Department of Environmental Metagenomics, Research Center One Health Ruhr, University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany; Centre of Water and Environmental Research, University of Duisburg-Essen, Essen, Germany
| | - Julia K Nuy
- Department of Environmental Metagenomics, Research Center One Health Ruhr, University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany; Centre of Water and Environmental Research, University of Duisburg-Essen, Essen, Germany
| | - Louisa Rothe
- Centre of Water and Environmental Research, University of Duisburg-Essen, Essen, Germany
| | - Tom L Stach
- Department of Environmental Metagenomics, Research Center One Health Ruhr, University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany; Centre of Water and Environmental Research, University of Duisburg-Essen, Essen, Germany
| | | | - Stefan Leuko
- German Aerospace Center, Institute of Aerospace Medicine, Cologne, Germany
| | | | - Ralf Möller
- German Aerospace Center, Institute of Aerospace Medicine, Cologne, Germany
| | - Marius Conrady
- Faculty of Life Sciences, Biosystemtechnik, Humboldt University Berlin, Berlin, Germany
| | - Markus Huth
- Faculty of Life Sciences, Biosystemtechnik, Humboldt University Berlin, Berlin, Germany
| | - Thomas Trabold
- Chair of Energy Process Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nürnberg, Germany
| | - Katharina Herkendell
- Chair of Energy Process Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nürnberg, Germany; Department of Energy Process Engineering and Conversion Technologies for Renewable Energies, Technische Universität Berlin, Berlin, Germany
| | - Alexander J Probst
- Department of Environmental Metagenomics, Research Center One Health Ruhr, University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany; Centre of Water and Environmental Research, University of Duisburg-Essen, Essen, Germany.
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5
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Yang Y, Wang W, Hu Q, Yao X, Yang W, Wen S, Wu H, Jin J, Shen L. Conversion of coastal wetlands to paddy fields substantially decreases methane oxidation potential and methanotrophic abundance on the eastern coast of China. WATER RESEARCH 2025; 272:122962. [PMID: 39674140 DOI: 10.1016/j.watres.2024.122962] [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: 08/21/2024] [Revised: 11/28/2024] [Accepted: 12/10/2024] [Indexed: 12/16/2024]
Abstract
Coastal wetland ecosystems play a key role in the global carbon cycle and climate mitigation. The land conversion of coastal wetlands to paddy fields, an increasingly common practice to feed the growing population, has been shown to dramatically stimulate the methane emissions of (CH4). However, the knowledge about how such wetland conversion affects the methane oxidation, a key process regulating methane emissions from coastal wetlands, is nearly unknown. In this study, a space-for-time substitution method was employed to investigate the impact of the conversion of coastal wetlands (dominated by Phragmites or mangrove (Kandelia and Bruguiera)) to paddy fields on the methane oxidation process on the eastern coast of China. Our results showed that the average CH4 oxidation potential in the converted paddy soils significantly reduced by 28.4 % and 29.3 %, respectively, and the average abundance of methanotrophic pmoA gene decreased by 77.1 % and 81.9 %, respectively, compared to the original Phragmites and mangrove soils. Significant changes in the methanotrophic community composition were also found after converting Phragmites and mangrove wetlands to paddy fields. Structural equation modeling analysis suggested that the land conversion significantly affected the CH4 oxidation potential by changing the soil physicochemical properties (pH, ammonium content, and nitrate content) and methanotrophic abundance. Overall this study showed significant alterations in CH4 oxidation potential and community composition and abundance of methanotrophs caused by conversion of coastal wetlands to paddy fields, improving the knowledge of the underlying microbial mechanisms of land conversion on methane emissions.
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Affiliation(s)
- Yuling Yang
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Weiqi Wang
- Key Laboratory of Humid Subtropical Eco-geographical Process, Ministry of Education, Fujian Normal University, Fuzhou, 350117, China
| | - Qinan Hu
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Xiaochen Yao
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Wangting Yang
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Sile Wen
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Haikun Wu
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Jinghao Jin
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Lidong Shen
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China.
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Zhao J, Wang D, Wang C, Lin Y, Ye H, Maung AT, El-Telbany M, Masuda Y, Honjoh KI, Miyamoto T, Xiao F. Biocontrol of Salmonella Schwarzengrund and Escherichia coli O157:H7 planktonic and biofilm cells via combined treatment of polyvalent phage and sodium hexametaphosphate on foods and food contact surfaces. Food Microbiol 2025; 126:104680. [PMID: 39638444 DOI: 10.1016/j.fm.2024.104680] [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: 06/24/2024] [Revised: 10/31/2024] [Accepted: 11/04/2024] [Indexed: 12/07/2024]
Abstract
Salmonella Schwarzengrund and Escherichia coli O157:H7 are ones of foodborne pathogens that can produce biofilms and cause serious food poisoning. Bacteriophages are an emerging antibacterial strategy used to prevent foodborne pathogen contamination in the food industry. In this study, the combined antibacterial effects of the polyvalent phage PS5 and sodium hexametaphosphate (SHMP) against both pathogens were investigated to evaluate their effectiveness in food applications. The combined treatment with phage PS5 (multiplicity of infection, MOI = 10) and 1.0% SHMP inhibited the growth of S. Schwarzengrund and E. coli O157:H7, and the viable counts of both decreased by more than 2.45 log CFU/mL. In KAGOME vegetable and fruit mixed juice, the combined treatment with PS5 (MOI = 100) and 1.0% SHMP also resulted in significant pathogen inactivation at 4 °C after 24 h. PS5 (1010 PFU/mL) and 1.0% SHMP showed stronger synergistic effects on biofilm formation and the removal of established biofilms on polystyrene plates. Additionally, we evaluated their combined effects on reducing the biofilms of S. Schwarzengrund and E. coli O157:H7 on glass tubes and cabbage leaves at 4 °C. These findings indicate the utility of this approach in the biocontrol of the planktonic and biofilm cells of S. Schwarzengrund and E. coli O157:H7 on foods and food contact surfaces.
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Affiliation(s)
- Junxin Zhao
- Food and Pharmacy College, Xuchang University, Xuchang, 461000, China
| | - Deguo Wang
- Food and Pharmacy College, Xuchang University, Xuchang, 461000, China
| | - Chen Wang
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Yunzhi Lin
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Haomin Ye
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Aye Thida Maung
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Mohamed El-Telbany
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Yoshimitsu Masuda
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Ken-Ichi Honjoh
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Takahisa Miyamoto
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan.
| | - Fugang Xiao
- Food and Pharmacy College, Xuchang University, Xuchang, 461000, China.
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7
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Li Y, Wang L, Chen S. An overview of the progress made in research into the Mpox virus. Med Res Rev 2025; 45:788-812. [PMID: 39318037 DOI: 10.1002/med.22085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 08/05/2024] [Accepted: 09/01/2024] [Indexed: 09/26/2024]
Abstract
Mpox is a zoonotic illness caused by the Mpox virus (MPXV), a member of the Orthopoxvirus family. Although a few cases have been reported outside Africa, it was originally regarded as an endemic disease limited to African countries. However, the Mpox outbreak of 2022 was remarkable in that the infection spread to more than 123 countries worldwide, causing thousands of infections and deaths. The ongoing Mpox outbreak has been declared as a public health emergency of international concern by the World Health Organization. For a better management and control of the epidemic, this review summarizes the research advances and important scientific findings on MPXV by reviewing the current literature on epidemiology, clinical characteristics, diagnostic methods, prevention and treatment measures, and animal models of MPXV. This review provides useful information to raise awareness about the transmission, symptoms, and protective measures of MPXV, serving as a theoretical guide for relevant institutions to control MPXV.
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Affiliation(s)
- Yansheng Li
- Shenzhen Key Laboratory of Microbiology in Genomic Modification & Editing and Application, Medical Innovation Technology Transformation Center of Shenzhen Second People's Hospital, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound lmaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Department of Critical Care Medicine, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Lianrong Wang
- Department of Respiratory Diseases, Institute of Pediatrics, Shenzhen Children's Hospital, Shenzhen, Guangdong, China
| | - Shi Chen
- Shenzhen Key Laboratory of Microbiology in Genomic Modification & Editing and Application, Medical Innovation Technology Transformation Center of Shenzhen Second People's Hospital, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound lmaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Department of Critical Care Medicine, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
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8
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Wang Y, Liu X, Huang C, Han W, Gu P, Jing R, Yang Q. Antibiotic resistance genes and virulence factors in the plastisphere in wastewater treatment plant effluent: Health risk quantification and driving mechanism interpretation. WATER RESEARCH 2025; 271:122896. [PMID: 39631158 DOI: 10.1016/j.watres.2024.122896] [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: 08/01/2024] [Revised: 11/04/2024] [Accepted: 11/29/2024] [Indexed: 12/07/2024]
Abstract
Microplastics (MPs) are ubiquitous in wastewater treatment plants (WWTPs) and provide a unique niche for the spread of pollutants. To date, risk assessments and driving mechanisms of pathogens, antibiotic resistance genes (ARGs), and virulence factors (VFs) in the plastisphere are still lacking. Here, the microbiota, ARGs, VFs, their potential health risks, and biologically driving mechanisms on polythene (PE), polyethylene terephthalate (PET), poly (butyleneadipate-co-terephthalate) and polylactic acid blends (PBAT/PLA), PLA MPs, and gravel in WWTP effluent were investigated. The results showed that plastisphere and gravel biofilm harbored more distinctive microorganisms, promoting the uniqueness of pathogens, ARGs, and VFs compared to WWTP effluent. The abundance of major pathogens, ARGs, and VFs in the plastisphere was 1.01-1.35 times higher than that in the effluent. The high health risk of ARGs (HRA) calculated by fully considering the abundance, clinical relevance, pathogenicity, accessibility and mobility, and the high proportion of resistance contigs with mobile genetic elements confirmed that the plastisphere posed the highest potential health risk. Candidatus Microthrix and Candidatus Promineifilum were the essential hosts of ARGs and VFs in the plastisphere and gravel biofilm, respectively. High metabolic activity such as amino acid metabolism and biosynthesis of secondary metabolites, and highly expressed key genes increased the synthesis of ARGs and VFs. The primary mechanisms driving ARG enrichment in the plastisphere were enhanced microbial metabolic activity, increased frequency of horizontal gene transfer, heightened antibiotic inactivation and efflux, and reduced cell permeability. This study provided new insights into the ARGs, VFs, and health risks of the plastisphere and emphasized the importance of strict control of wastewater discharge.
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Affiliation(s)
- Yaxin Wang
- Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing, 100124, China
| | - Xiuhong Liu
- Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing, 100124, China.
| | - Chenduo Huang
- Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing, 100124, China
| | - Weipeng Han
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing, 100124, China
| | - Pengchao Gu
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing, 100124, China
| | - Ruxian Jing
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing, 100124, China
| | - Qing Yang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing, 100124, China
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Achterberg T, de Jong A. ProPr54 web server: predicting σ 54 promoters and regulon with a hybrid convolutional and recurrent deep neural network. NAR Genom Bioinform 2025; 7:lqae188. [PMID: 39781509 PMCID: PMC11704786 DOI: 10.1093/nargab/lqae188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 11/19/2024] [Accepted: 12/23/2024] [Indexed: 01/12/2025] Open
Abstract
σ54 serves as an unconventional sigma factor with a distinct mechanism of transcription initiation, which depends on the involvement of a transcription activator. This unique sigma factor σ54 is indispensable for orchestrating the transcription of genes crucial to nitrogen regulation, flagella biosynthesis, motility, chemotaxis and various other essential cellular processes. Currently, no comprehensive tools are available to determine σ54 promoters and regulon in bacterial genomes. Here, we report a σ54 promoter prediction method ProPr54, based on a convolutional neural network trained on a set of 446 validated σ54 binding sites derived from 33 bacterial species. Model performance was tested and compared with respect to bacterial intergenic regions, demonstrating robust applicability. ProPr54 exhibits high performance when tested on various bacterial species, highly surpassing other available σ54 regulon identification methods. Furthermore, analysis on bacterial genomes, which have no experimentally validated σ54 binding sites, demonstrates the generalization of the model. ProPr54 is the first reliable in silico method for predicting σ54 binding sites, making it a valuable tool to support experimental studies on σ54. In conclusion, ProPr54 offers a reliable, broadly applicable tool for predicting σ54 promoters and regulon genes in bacterial genome sequences. A web server is freely accessible at http://propr54.molgenrug.nl.
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Affiliation(s)
- Tristan Achterberg
- Department of Molecular Genetics, Groningen, Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Anne de Jong
- Department of Molecular Genetics, Groningen, Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands
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Jha K, Jaishwal P, Yadav TP, Singh SP. Self-assembling of coiled-coil peptides into virus-like particles: Basic principles, properties, design, and applications with special focus on vaccine design and delivery. Biophys Chem 2025; 318:107375. [PMID: 39674128 DOI: 10.1016/j.bpc.2024.107375] [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: 10/01/2024] [Revised: 12/03/2024] [Accepted: 12/03/2024] [Indexed: 12/16/2024]
Abstract
Self-assembling peptide nanoparticles (SAPN) based delivery systems, including virus-like particles (VLP), have shown great potential for becoming prominent in next-generation vaccine and drug development. The VLP can mimic properties of natural viral capsid in terms of size (20-200 nm), geometry (i.e., icosahedral structures), and the ability to generate a robust immune response (with multivalent epitopes) through activation of innate and/or adaptive immune signals. In this regard, coiled-coil (CC) domains are suitable building blocks for designing VLP because of their programmable interaction specificity, affinity, and well-established sequence-to-structure relationships. Generally, two CC domains with different oligomeric states (trimer and pentamer) are fused to form a monomeric protein through a short, flexible spacer sequence. By using combinations of symmetry axes (2-, 3- and 5- folds) that are unique to the geometry of the desired protein cage, it is possible, in principle, to assemble well-defined protein cages like VLP. In this review, we have discussed the crystallographic rules and the basic principles involved in the design of CC-based VLP. It also explored the functions of numerous noncovalent interactions in generating stable VLP structures, which play a crucial role in improving the properties of vaccine immunogenicity, drug delivery, and 3D cell culturing.
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Affiliation(s)
- Kisalay Jha
- Department of Biotechnology, Mahatma Gandhi Central University, Motihari 845401, India
| | - Puja Jaishwal
- Department of Biotechnology, Mahatma Gandhi Central University, Motihari 845401, India
| | - Thakur Prasad Yadav
- Department of Physics, Faculty of Science, University of Allahabad, Prayagraj 211002, India.
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Liao M, Gong H, Ge T, Shen K, Campana M, McBain AJ, Wu C, Hu X, Lu JR. Probing antimicrobial synergy by novel lipopeptides paired with antibiotics. J Colloid Interface Sci 2025; 681:82-94. [PMID: 39591858 DOI: 10.1016/j.jcis.2024.11.169] [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: 08/23/2024] [Revised: 10/27/2024] [Accepted: 11/21/2024] [Indexed: 11/28/2024]
Abstract
Antimicrobial resistance (AMR) is fast becoming a major global challenge in both hospital and community settings as many current antibiotics and treatment processes are under the threat of being rendered less effective or ineffective. Synergistic combination of an antibiotic and an aiding agent with a different set of properties provides an important but largely unexploited option to 'repurpose' existing biomaterial's space while addressing issues of potency, spectrum, toxicity and resistance in early stages of antimicrobial drug discovery. This work explores how to combine tetracycline/minocycline (TC/MC) with a broad-spectrum antimicrobial lipopeptide that has been designed to improve the efficiency of membrane targeting and intramembrane accumulation, thereby enhancing antimicrobial efficacy. Experimental measurements of fractional inhibition concentration index (FICI) were undertaken from binary antibiotic-lipopeptide combinations. Most FICI values were found to be lower than 0.5 against both Gram-positive and Gram-negative bacterial strains studied including 3 AMR strains, revealing strong synergetic effects via favorable membrane-lytic interactions. The antimicrobial actions of this type of binary combinations are featured by the fast time-killing and high TC/MC uptake, benefited from effective membrane-lytic disruptions by the lipopeptide. This study thus provides an important mechanistic understanding of the combined antibiotic-lipopeptide approach to improve the therapeutic potential of conventional antibiotics by illustrating how amphiphilic lipopeptide-antibiotic combinations interact with biological membranes, providing a promising alternative to combat AMR through rational design of lipopeptide as an aiding agent.
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Affiliation(s)
- Mingrui Liao
- Biological Physics Laboratory, Department of Physics and Astronomy, School of Natural Science, The University of Manchester, Oxford Road, Manchester M13 9PL UK
| | - Haoning Gong
- Biological Physics Laboratory, Department of Physics and Astronomy, School of Natural Science, The University of Manchester, Oxford Road, Manchester M13 9PL UK
| | - Tianhao Ge
- Biological Physics Laboratory, Department of Physics and Astronomy, School of Natural Science, The University of Manchester, Oxford Road, Manchester M13 9PL UK
| | - Kangcheng Shen
- Biological Physics Laboratory, Department of Physics and Astronomy, School of Natural Science, The University of Manchester, Oxford Road, Manchester M13 9PL UK
| | - Mario Campana
- ISIS Pulsed Neutron & Muon Source, STFC Rutherford Appleton Laboratory, Didcot OX11 0QX, UK
| | - Andrew J McBain
- Division of Pharmacy and Optometry, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Chunxian Wu
- School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Xuzhi Hu
- State Key Laboratory of Solid Lubrication, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, PR China.
| | - Jian R Lu
- Biological Physics Laboratory, Department of Physics and Astronomy, School of Natural Science, The University of Manchester, Oxford Road, Manchester M13 9PL UK.
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12
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Xia Q, Qiu Q, Cheng J, Huang W, Yi X, Yang F, Huang W. Microbially mediated iron redox processes for carbon and nitrogen removal from wastewater: Recent advances. BIORESOURCE TECHNOLOGY 2025; 419:132041. [PMID: 39765277 DOI: 10.1016/j.biortech.2025.132041] [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: 11/05/2024] [Revised: 12/23/2024] [Accepted: 01/04/2025] [Indexed: 01/11/2025]
Abstract
Iron is the most abundant redox-active metal on Earth. The microbially mediated iron redox processes, including dissimilatory iron reduction (DIR), ammonium oxidation coupled with Fe(III) reduction (Feammox), Fe(III) dependent anaerobic oxidation of methane (Fe(III)-AOM), nitrate-reducing Fe(II) oxidation (NDFO), and Fe(II) dependent dissimilatory nitrate reduction to ammonium (Fe(II)-DNRA), play important parts in carbon and nitrogen biogeochemical cycling globally. In this review, the reaction mechanisms, electron transfer pathways, functional microorganisms, and characteristics of these processes are summarized; the prospective applications for carbon and nitrogen removal from wastewater are reviewed and discussed; and the research gaps and future directions of these processes for the treatment of wastewater are also underlined. This review is expected to give new insights into the development of economic and environmentally friendly iron-based wastewater treatment procedures.
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