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Kang Y, Wang J, Wang Y, Li Z. Profiles of phage in global hospital wastewater: Association with microbial hosts, antibiotic resistance genes, metal resistance genes, and mobile genetic elements. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171766. [PMID: 38513871 DOI: 10.1016/j.scitotenv.2024.171766] [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: 12/24/2023] [Revised: 02/28/2024] [Accepted: 03/15/2024] [Indexed: 03/23/2024]
Abstract
Hospital wastewater (HWW) is known to host taxonomically diverse microbial communities, yet limited information is available on the phages infecting these microorganisms. To fill this knowledge gap, we conducted an in-depth analysis using 377 publicly available HWW metagenomic datasets from 16 countries across 4 continents in the NCBI SRA database to elucidate phage-host dynamics and phage contributions to resistance gene transmission. We first assembled a metagenomic HWW phage catalog comprising 13,812 phage operational taxonomic units (pOTUs). The majority of these pOTUs belonged to the Caudoviricetes order, representing 75.29 % of this catalog. Based on the lifestyle of phages, we found that potentially virulent phages predominated in HWW. Specifically, 583 pOTUs have been predicted to have the capability to lyse 81 potentially pathogenic bacteria, suggesting the promising role of HWW phages as a viable alternative to antibiotics. Among all pOTUs, 1.56 % of pOTUs carry 108 subtypes of antibiotic resistance genes (ARGs), 0.96 % of pOTUs carry 76 subtypes of metal resistance genes (MRGs), and 0.96 % of pOTUs carry 22 subtypes of non-phage mobile genetic elements (MGEs). Predictions indicate that certain phages carrying ARGs, MRGs, and non-phage MGEs could infect bacteria hosts, even potential pathogens. This suggests that phages in HWW may contribute to the dissemination of resistance-associated genes in the environment. This meta-analysis provides the first global catalog of HWW phages, revealing their correlations with microbial hosts and pahge-associated ARGs, MRG, and non-phage MGEs. The insights gained from this research hold promise for advancing the applications of phages in medical and industrial contexts.
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Affiliation(s)
- Yutong Kang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102200, China
| | - Jie Wang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Yuan Wang
- North China University of Science and Technology, Basic Medical College, Tangshan, Hebei 063210, P.R. China
| | - Zhenjun Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102200, China.
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Zhang X, Hua J, Song Z, Li K. A review: Marine aquaculture impacts marine microbial communities. AIMS Microbiol 2024; 10:239-254. [PMID: 38919720 PMCID: PMC11194620 DOI: 10.3934/microbiol.2024012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 03/04/2024] [Accepted: 03/14/2024] [Indexed: 06/27/2024] Open
Abstract
Marine aquaculture is key for protein production but disrupts marine ecosystems by releasing excess feed and pharmaceuticals, thus affecting marine microbes. Though vital, its environmental impact often remains overlooked. This article delves into mariculture's effects on marine microbes, including bacteria, fungi, viruses, and antibiotic-resistance genes in seawater and sediments. It highlights how different mariculture practices-open, pond, and cage culture-affect these microbial communities. Mariculture's release of nutrients, antibiotics, and heavy metals alters the microbial composition, diversity, and functions. Integrated multi-trophic aquaculture, a promising sustainable approach, is still developing and needs refinement. A deep understanding of mariculture's impact on microbial ecosystems is crucial to minimize pollution and foster sustainable practices, paving the way for the industry's sustainable advancement.
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Affiliation(s)
| | | | | | - Kejun Li
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
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Zhang H, Zhang H, Du H, Yu X, Xu Y. The insights into the phage communities of fermented foods in the age of viral metagenomics. Crit Rev Food Sci Nutr 2024:1-13. [PMID: 38214674 DOI: 10.1080/10408398.2023.2299323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Phages play a critical role in the assembly and regulation of fermented food microbiome through lysis and lysogenic lifestyle, which in turn affects the yield and quality of fermented foods. Therefore, it is important to investigate and characterize the diversity and function of phages under complex microbial communities and nutrient substrate conditions to provide novel insights into the regulation of traditional spontaneous fermentation. Viral metagenomics has gradually garnered increasing attention in fermented food research to elucidate phage functions and characterize the interactions between phages and the microbial community. Advances in this technology have uncovered a wide range of phages associated with the production of traditional fermented foods and beverages. This paper reviews the common methods of viral metagenomics applied in fermented food research, and summarizes the ecological functions of phages in traditional fermented foods. In the future, combining viral metagenomics with culturable methods and metagenomics will broaden the scope of research on fermented food systems, revealing the complex role of phages and intricate phage-bacterium interactions.
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Affiliation(s)
- Huadong Zhang
- Laboratory of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Hongxia Zhang
- College of Life Sciences, Shanxi Normal University, Taiyuan, Shanxi, China
| | - Hai Du
- Laboratory of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Xiaowei Yu
- Laboratory of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yan Xu
- Laboratory of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
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Xiong L, Li Y, Zeng K, Wei Y, Li H, Ji X. Revealing viral diversity in the Napahai plateau wetland based on metagenomics. Antonie Van Leeuwenhoek 2023; 117:3. [PMID: 38153618 DOI: 10.1007/s10482-023-01912-2] [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: 08/30/2023] [Accepted: 11/22/2023] [Indexed: 12/29/2023]
Abstract
We focused on exploring the diversity of viruses in the Napahai plateau wetland, a unique ecosystem located in Yunnan, China. While viruses in marine environments have been extensively studied for their influence on microbial metabolism and biogeochemical cycles, little is known about their composition and function in plateau wetlands. Metagenomic analysis was employed to investigate the viral diversity and biogeochemical impacts in the Napahai wetland. It revealed that the Caudoviricetes and Malgrandaviricetes class level was the most abundant viral category based on phylogenetic analysis. Additionally, a gene-sharing network highlighted the presence of numerous unexplored viruses and demonstrated their unique characteristics and significant variation within the viral community of the Napahai wetland. Furthermore, the study identified the auxiliary metabolic genes (AMGs). AMGs provide phages with additional functions, such as protection against host degradation and involvement in metabolic pathways, such as the pentose phosphate pathway and DNA biosynthesis. The viruses in the Napahai wetland were found to influence carbon, nitrogen, sulfur, and amino acid metabolism, indirectly contributing to biogeochemical cycling through these AMGs. Overall, the research sheds light on the diverse and unique viral communities in the Napahai plateau wetland and emphasizes the significant roles of viruses in microbial ecology. The findings contribute to a deeper understanding of the characteristics and ecological functions of viral communities in plateau wetland ecosystems.
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Affiliation(s)
- Lingling Xiong
- Faculty of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Yanmei Li
- Faculty of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Kun Zeng
- Faculty of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Yunlin Wei
- Faculty of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Haiyan Li
- Medical School, Kunming University of Science and Technology, Kunming, 650500, China.
| | - Xiuling Ji
- Faculty of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China.
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Mendoza-Cano F, Encinas-García T, Muhlia-Almazán A, Porchas-Cornejo M, de la Re-Vega E, Sánchez-Paz A. Development and validation of a real-time PCR assay protocol for the specific detection and quantification of pelagiphages in seawater samples. MARINE ENVIRONMENTAL RESEARCH 2023; 191:106168. [PMID: 37708616 DOI: 10.1016/j.marenvres.2023.106168] [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: 05/18/2023] [Revised: 08/31/2023] [Accepted: 09/02/2023] [Indexed: 09/16/2023]
Abstract
Earth is inhabited by numerous adaptations of cellular forms shaped by the persistent scrutiny of natural selection. Thus, as natural selection has fixed beneficial adaptations of functional traits, cellular life has conquered almost all environmental niches on our planet. However, cellular life succumbs in number and genetic diversity to viruses. Among all viruses, phages are highly prevalent in diverse environments, and due to their vast genetic diversity and abundance, their relevant role as significant players in several ecological processes is now fully recognized. Pelagiphages, bacteriophages infecting bacteria of the SAR11 clade, are the most abundant viruses in the oceans. However, the ecological contribution of pelagiphages on populations of Pelagibacterales remains largely underestimated. An essential aspect of estimating the impact of bacteriophages is their absolute and precise quantification, which provides relevant information about the host-virus interactions and the structure of viral assemblages. Consequently, due to its abundance and claimed influence in the biogeochemical cycling of elements, the accurate quantification of pelagiphages results in an essential task. This study describes the development and validation of a sensitive, specific, accurate and reproducible qPCR platform targeting pelagiphages. Moreover, this method allowed the detection and quantification of pelagiphages in the Gulf of California for the first time.
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Affiliation(s)
- F Mendoza-Cano
- Laboratorio de Virología, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), S.C. (Campus Hermosillo), Calle Hermosa 101, Fraccionamiento Los Ángeles, Hermosillo, Sonora, C.P. 83206, México
| | - T Encinas-García
- Laboratorio de Virología, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), S.C. (Campus Hermosillo), Calle Hermosa 101, Fraccionamiento Los Ángeles, Hermosillo, Sonora, C.P. 83206, México; Departamento de Investigaciones Científicas y Tecnológicas (DICTUS), Universidad de Sonora, Hermosillo, Sonora, 83000, México
| | - A Muhlia-Almazán
- Bioenergetics and Molecular Genetics Lab, Centro de Investigación en Alimentación y Desarrollo (CIAD), A. C. Carretera Gustavo Enrique Astiazarán Rosas, No. 46, Col. La Victoria, Hermosillo, Sonora, 83304, México
| | - M Porchas-Cornejo
- Centro de Investigaciones Biológicas del Noroeste, S.C. Km 2.35 Carretera a Las Tinajas, S/N Colonia Tinajas, Guaymas, Sonora, C.P. 85460, México
| | - E de la Re-Vega
- Departamento de Investigaciones Científicas y Tecnológicas (DICTUS), Universidad de Sonora, Hermosillo, Sonora, 83000, México
| | - A Sánchez-Paz
- Laboratorio de Virología, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), S.C. (Campus Hermosillo), Calle Hermosa 101, Fraccionamiento Los Ángeles, Hermosillo, Sonora, C.P. 83206, México.
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Diversity and potential function of pig gut DNA viruses. Heliyon 2023; 9:e14020. [PMID: 36915549 PMCID: PMC10006684 DOI: 10.1016/j.heliyon.2023.e14020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
Viruses are ubiquitous in the gut of animals and play an important role in the ecology of the gut microbiome. The potential effects of these substances on the growth and development of the body are not fully known. Little is known about the effects of breeding environment on pig gut virome. Here, there are 3584 viral operational taxonomic units (vOTUs) longer than 5 kb identified by virus-enriched metagenome sequencing from 25 pig fecal samples. Only a small minority of vOTUs (11.16%) can be classified at the family level, and ∼50% of the genes could be annotated, supporting the concept of pig gut as reservoirs of substantial undescribed viral genetic diversity. The composition of pig gut virome in the six regions may be related to geography. There are only 20 viral clusters (VCs) shared among pig gut virome in six regions of Shanxi Province. These viruses rarely carry antibiotic resistance genes (ARGs). At the same time, they possess abundant auxiliary metabolic genes (AMGs) potentially involved in carbon, sulfur metabolism and cofactor biosynthesis, etc. This study has revealed the unique characteristics and potential function of pig gut DNA virome and established a foundation for the recognition of the viral roles in gut environment.
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Li Y, Xiong L, Yu H, Xiang Y, Wei Y, Zhang Q, Ji X. Biogeochemical sulfur cycling of virus auxiliary metabolic genes involved in Napahai plateau wetland. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:44430-44438. [PMID: 36692711 DOI: 10.1007/s11356-023-25408-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 01/15/2023] [Indexed: 01/25/2023]
Abstract
Virus plays important roles in regulating microbial community structure, horizontal gene transfer, and promoting biological evolution, also augmenting host metabolism during infection via the expression of auxiliary metabolic genes (AMGs), and thus affect biogeochemical cycling in the oceans. As the "kidney of the earth," wetlands have rich biodiversity and abundant resources. Based on metagenomic data, 10 AMGs associated with sulfur cycling, i.e., tusA, moaD, dsrE, soxA, soxB, soxC, soxD, soxX, soxY, and soxZ, were analyzed in Napahai plateau wetland. The phylogenetic trees of AMGs involved in sulfur metabolism from different habitats and host origins were constructed. Combined with principal coordinate analysis, it revealed that most AMGs associated with sulfur metabolism clustered separately, indicating the abundance and uniqueness in this region. The sulfur metabolism pathways involved by AMGs were mainly SOX systems, among which sulfur oxidation was associated with moaD and dsrE genes, while sulfur transport was related to tusA genes. It provides an insight into the biogeochemical sulfur cycling in plateau wetlands and lays the foundation for further study on the co-evolution of virus and host.
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Affiliation(s)
- Yanmei Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Lingling Xiong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Hang Yu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Yingying Xiang
- Department of Stomatology, Yan'an Hospital Affiliated to Kunming Medical University, Kunming, 650031, China
| | - Yunlin Wei
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Qi Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Xiuling Ji
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China.
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Zhou D, Liu S, Guo G, He X, Xing C, Miao Q, Chen G, Chen X, Yan H, Zeng J, Zheng Z, Deng H, Weng S, He J. Virome Analysis of Normal and Growth Retardation Disease-Affected Macrobrachium rosenbergii. Microbiol Spectr 2022; 10:e0146222. [PMID: 36445118 PMCID: PMC9769563 DOI: 10.1128/spectrum.01462-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 11/10/2022] [Indexed: 11/30/2022] Open
Abstract
The giant freshwater prawn, Macrobrachium rosenbergii, is an important aquaculture species in China. Growth retardation disease (GRD) is a common contagious disease in M. rosenbergii, resulting in slow growth and precocious puberty in prawns, and has caused growing economic losses in the M. rosenbergii industry. To investigate the viral diversity of M. rosenbergii and identify potentially high-risk viruses linked to GRD, virome analysis of the GRD-affected and normal M. rosenbergii was carried out using next-generation sequencing (NGS). A total of 327 contigs (>500 bp) were related to viral sequences belonging to 23 families/orders and a group of unclassified viruses. The majority of the viral contigs in M. rosenbergii belonged to the order Picornavirales, with the Solinviviridae family being the most abundant in both the diseased and normal groups. Furthermore, 16 RNA viral sequences with nearly complete genomes were characterized and phylogenetically analyzed, belonging to the families Solinviviridae, Flaviviridae, Polycipiviridae, Marnaviridae, and Dicistroviridae as well as three new clades of the order Picornavirales. Notably, the cross-species transmission of a picorna-like virus was observed between M. rosenbergii and plants. The "core virome" seemed to be present in the diseased and normal prawns. Still, a clear difference in viral abundance was observed between the two groups. These results showed that the broad diversity of viruses is present in M. rosenbergii and that the association between viruses and disease of M. rosenbergii needs to be further investigated. IMPORTANCE Growth retardation disease (GRD) has seriously affected the development and economic growth of the M. rosenbergii aquaculture industry. Our virome analysis showed that diverse viral sequences were present in M. rosenbergii, significantly expanding our knowledge of viral diversity in M. rosenbergii. Some differences in viral composition were noted between the diseased and normal prawns, indicating that some viruses become more abundant in occurrences or outbreaks of diseases. In the future, more research will be needed to determine which viruses pose a risk for M. rosenbergii. Our study provides important baseline information contributing to disease surveillance and risk assessment in M. rosenbergii aquaculture.
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Affiliation(s)
- Dandan Zhou
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shanshan Liu
- School of Ecology, Sun Yat-sen University, Guangzhou, China
| | - Guangyu Guo
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xinyi He
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | | | - Qijin Miao
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Gongrui Chen
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xiaolin Chen
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Hongyu Yan
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jiamin Zeng
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhenwen Zheng
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Hengwei Deng
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Shaoping Weng
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jianguo He
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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