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Pardo A, Villasante A, Romero J. Skin Microbial Community Associated to Strawberry Disease in Farmed Rainbow Trout ( Oncorhynchus mykiss Walbaum, 1792). Microorganisms 2024; 12:217. [PMID: 38276202 PMCID: PMC10818565 DOI: 10.3390/microorganisms12010217] [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: 12/29/2023] [Revised: 01/19/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
Aquaculture plays a crucial role in addressing the growing global demand for food. However, diseases associated with intensive aquaculture practices, especially those affecting the skin, can present significant challenges to both fish health and the industry as a whole. Strawberry disease (SD), also known as red-mark syndrome, is a persistent and non-lethal skin condition observed in Rainbow Trout (Oncorhynchus mykiss) in the United States and various European countries. SD is a nonlethal skin condition of an unclear etiology that affects rainbow trout reared in freshwater close to the harvest period. We used a RNA-based approach to examine active microbiota in the SD skin lesions and compared to non-injured skin. Our results, based on using 16S rRNA gene next-generation sequencing, showed that the skin microbiota was dominated by the phyla Firmicutes, Proteobacteria, and Actinobacteria. The comparisons of the skin microbiota between injured and non-injured samples showed differences in the alpha diversity (Fisher index) and beta diversity metrics (ANOSIM). At the genus level, both Pseudomonas and Candidatus Midichloria were highlighted as the most abundant taxa detected in samples obtained from fish affected with strawberry diseases. In contrast, the most abundant taxa in non-injured skin were Escherichia-Shigella, Streptococcus, and Pseudoalteromonas. In conclusion, our study on SD revealed distinct differences in the microbiota composition between skin lesions and non-injured skin. This is the first description of microbiota associated with SD-injured skin samples using an RNA approach.
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Affiliation(s)
- Alda Pardo
- Laboratorio de Biotecnología de Alimentos, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, El Líbano 5524, Santiago 7830489, Chile; (A.P.); (A.V.)
- Cooperative Program for Aquaculture (Ph.D.), Universidad de Chile, Universidad Católica del Norte, Pontificia Universidad Católica de Valparaíso, Valparaíso 2340025, Chile
| | - Alejandro Villasante
- Laboratorio de Biotecnología de Alimentos, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, El Líbano 5524, Santiago 7830489, Chile; (A.P.); (A.V.)
- Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Santiago 7500000, Chile
| | - Jaime Romero
- Laboratorio de Biotecnología de Alimentos, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, El Líbano 5524, Santiago 7830489, Chile; (A.P.); (A.V.)
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Lorgen-Ritchie M, Uren Webster T, McMurtrie J, Bass D, Tyler CR, Rowley A, Martin SAM. Microbiomes in the context of developing sustainable intensified aquaculture. Front Microbiol 2023; 14:1200997. [PMID: 37426003 PMCID: PMC10327644 DOI: 10.3389/fmicb.2023.1200997] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/08/2023] [Indexed: 07/11/2023] Open
Abstract
With an ever-growing human population, the need for sustainable production of nutritional food sources has never been greater. Aquaculture is a key industry engaged in active development to increase production in line with this need while remaining sustainable in terms of environmental impact and promoting good welfare and health in farmed species. Microbiomes fundamentally underpin animal health, being a key part of their digestive, metabolic and defense systems, in the latter case protecting against opportunistic pathogens in the environment. The potential to manipulate the microbiome to the advantage of enhancing health, welfare and production is an intriguing prospect that has gained considerable traction in recent years. In this review we first set out what is known about the role of the microbiome in aquaculture production systems across the phylogenetic spectrum of cultured animals, from invertebrates to finfish. With a view to reducing environmental footprint and tightening biological and physical control, investment in "closed" aquaculture systems is on the rise, but little is known about how the microbial systems of these closed systems affect the health of cultured organisms. Through comparisons of the microbiomes and their dynamics across phylogenetically distinct animals and different aquaculture systems, we focus on microbial communities in terms of their functionality in order to identify what features within these microbiomes need to be harnessed for optimizing healthy intensified production in support of a sustainable future for aquaculture.
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Affiliation(s)
| | - Tamsyn Uren Webster
- Centre for Sustainable Aquatic Research, Swansea University, Swansea, United Kingdom
| | - Jamie McMurtrie
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - David Bass
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth, United Kingdom
| | - Charles R. Tyler
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Andrew Rowley
- Department of Biosciences, Faculty of Science and Engineering, Swansea University, Swansea, United Kingdom
| | - Samuel A. M. Martin
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
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Lan X, Peng X, Du T, Xia Z, Gao Q, Tang Q, Yi S, Yang G. Alterations of the Gut Microbiota and Metabolomics Associated with the Different Growth Performances of Macrobrachium rosenbergii Families. Animals (Basel) 2023; 13:ani13091539. [PMID: 37174576 PMCID: PMC10177557 DOI: 10.3390/ani13091539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
To investigate the key gut microbiota and metabolites associated with the growth performance of Macrobrachium rosenbergii families, 16S rRNA sequencing and LC-MS metabolomic methods were used. In this study, 90 M. rosenbergii families were bred to evaluate growth performance. After 92 days of culture, high (H), medium (M), and low (L) experimental groups representing three levels of growth performance, respectively, were collected according to the weight gain and specific growth rate of families. The composition of gut microbiota showed that the relative abundance of Firmicutes, Lachnospiraceae, Lactobacillus, and Blautia were much higher in Group H than those in M and L groups. Meanwhile, compared to the M and L groups, Group H had significantly higher levels of spermidine, adenosine, and creatinine, and lower levels of L-citrulline. Correlation analysis showed that the abundances of Lactobacillus and Blautia were positively correlated with the levels of alpha-ketoglutaric acid and L-arginine. The abundance of Blautia was also positively correlated with the levels of adenosine, taurine, and spermidine. Notably, lots of metabolites related to the metabolism and biosynthesis of arginine, taurine, hypotaurine, and fatty acid were upregulated in Group H. This study contributes to figuring out the landscape of the gut microbiota and metabolites associated with prawn growth performance and provides a basis for selective breeding.
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Affiliation(s)
- Xuan Lan
- Zhejiang Provincial Key Laboratory of Aquatic Resources Conservation and Development, Key Laboratory of Aquatic Animal Genetic Breeding and Nutrition, Chinese Academy of Fishery Sciences, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Xin Peng
- Zhejiang Provincial Key Laboratory of Aquatic Resources Conservation and Development, Key Laboratory of Aquatic Animal Genetic Breeding and Nutrition, Chinese Academy of Fishery Sciences, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Tingting Du
- Zhejiang Provincial Key Laboratory of Aquatic Resources Conservation and Development, Key Laboratory of Aquatic Animal Genetic Breeding and Nutrition, Chinese Academy of Fishery Sciences, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Zhenglong Xia
- Jiangsu Shufeng Prawn Breeding Co., Ltd., Gaoyou 225654, China
| | - Quanxin Gao
- Zhejiang Provincial Key Laboratory of Aquatic Resources Conservation and Development, Key Laboratory of Aquatic Animal Genetic Breeding and Nutrition, Chinese Academy of Fishery Sciences, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Qiongying Tang
- Zhejiang Provincial Key Laboratory of Aquatic Resources Conservation and Development, Key Laboratory of Aquatic Animal Genetic Breeding and Nutrition, Chinese Academy of Fishery Sciences, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Shaokui Yi
- Zhejiang Provincial Key Laboratory of Aquatic Resources Conservation and Development, Key Laboratory of Aquatic Animal Genetic Breeding and Nutrition, Chinese Academy of Fishery Sciences, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Guoliang Yang
- Zhejiang Provincial Key Laboratory of Aquatic Resources Conservation and Development, Key Laboratory of Aquatic Animal Genetic Breeding and Nutrition, Chinese Academy of Fishery Sciences, College of Life Sciences, Huzhou University, Huzhou 313000, China
- Jiangsu Shufeng Prawn Breeding Co., Ltd., Gaoyou 225654, China
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Cicala F, Cisterna-Céliz JA, Paolinelli M, Moore JD, Sevigny J, Rocha-Olivares A. The Role of Diversity in Mediating Microbiota Structural and Functional Differences in Two Sympatric Species of Abalone Under Stressed Withering Syndrome Conditions. MICROBIAL ECOLOGY 2023; 85:277-287. [PMID: 35064808 DOI: 10.1007/s00248-022-01970-5] [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: 06/25/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
Withering syndrome (WS) is a gastro-intestinal (GI) infectious disease likely affecting all abalone species worldwide. Structural and functional changes in abalone GI microbiotas under WS-stressed conditions remain poorly investigated. It is unclear if interspecific microbiota differences, such as the presence of certain microbes, their abundance, and functional capabilities, may be involved in the occurrence of this disease. Bacterial microbiotas of healthy Haliotis fulgens and Haliotis corrugata are mainly composed by Tenericutes, Proteobacteria, Fusobacteria, and Spirochaetes. We previously reported species-specific structural and functional profiles of those communities and suggested that they are of consequence to the different susceptibility of each species to WS. Here, we address this question by comparing the structure and function of healthy and dysbiotic microbiota through 454 pyrosequencing and PICRUSt 2, respectively. Our findings suggest that the extent to which WS-stressed conditions may explain structural and functional differences in GI microbiota is contingent on the microbiota diversity itself. Indeed, microbiota differences between stressed and healthy abalone were marginal in the more complex bacterial communities of H. corrugata, in which no significant structural or functional changes were detected. Conversely, significant structural changes were observed in the less complex bacterial microbiota of H. fulgens. Moreover, structural alterations led to a significant downregulation of some metabolic activities conducted by GI bacteria. Accordingly, results suggest that gastro-intestinal bacterial diversity appears to be related with both the health of abalone and the etiology of WS.
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Affiliation(s)
- Francesco Cicala
- Department of Biological Oceanography, CICESE, Carretera Tijuana-Ensenada km 3918, 22860, Ensenada, Baja CA, Mexico
- Department of Biomedical Innovation, CICESE, Carretera Tijuana-Ensenada km 3918, 22860, Ensenada, Baja CA, Mexico
| | | | - Marcos Paolinelli
- National Council of Scientific and Technical Research (CONICET), Av. Rivadavia 1917, C1033AAJ, Buenos Aires, Argentina
- National Institute of Agricultural Technology INTA EEA Mendoza, San Martin 3853, Luján de Cuyo, 5507, Mendoza, Argentina
| | - James D Moore
- Bodega Marine Laboratory, University of California at Davis, P.O. Box 247, Bodega Bay, CA, USA
| | - Joseph Sevigny
- Hubbard Center for Genome Studies, University of New Hampshire, 35 Colovos Rd, Durham, NH, 03824, USA
| | - Axayácatl Rocha-Olivares
- Department of Biological Oceanography, CICESE, Carretera Tijuana-Ensenada km 3918, 22860, Ensenada, Baja CA, Mexico.
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Plante CJ, Hill-Spanik KM, Emerson R. Inputs don't equal outputs: bacterial microbiomes of the ingesta, gut, and feces of the keystone deposit feeder Ilyanassa obsoleta. FEMS Microbiol Ecol 2022; 99:6887277. [PMID: 36496168 DOI: 10.1093/femsec/fiac152] [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: 04/19/2022] [Revised: 11/22/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
Bacteria drive energy fluxes and geochemical processes in estuarine sediments. Deposit-feeding invertebrates alter the structure and activity of microbial communities through sediment ingestion, gut passage, and defecation. The eastern mud snail, Ilyanassa obsoleta, is native to estuaries of the northwestern Atlantic, ranging from Nova Scotia, Canada, to Florida in the USA. Given extremely high densities, their deposit-feeding and locomotory activities exert ecological influence on other invertebrates and microbes. Our aim was to characterize the bacterial microbiome of this 'keystone species' and determine how its feeding alters the native bacterial microbiota. We gathered snails from both mudflat and sandflat habitats and collected their fresh fecal pellets in the laboratory. Dissection of these same snails allowed us to compare bacterial assemblages of ingested sediments, shell surfaces, gut sections (esophagus, stomach, intestine), and feces using DNA metabarcoding. Our findings indicate a diverse, resident gut microbiota. The stomach and intestines were dominated by bacteria of the genus Mycoplasma. Comparison of ingesta and feces revealed digestion of several bacterial taxa, introduction of gut residents during passage, in addition to unique bacterial taxa within the feces of unknown provenance. Our results demonstrate that I. obsoleta has the potential to modify microbial community structure in estuarine sediments.
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Affiliation(s)
- Craig J Plante
- Grice Marine Laboratory, College of Charleston, Charleston, SC 29412, United States
| | | | - Rowan Emerson
- Grice Marine Laboratory, College of Charleston, Charleston, SC 29412, United States
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Arboleda-Baena C, Pareja CB, Pla I, Logares R, De la Iglesia R, Navarrete SA. Hidden interactions in the intertidal rocky shore: variation in pedal mucus microbiota among marine grazers that feed on epilithic biofilm communities. PeerJ 2022; 10:e13642. [PMID: 36172502 PMCID: PMC9512015 DOI: 10.7717/peerj.13642] [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: 08/23/2021] [Accepted: 06/07/2022] [Indexed: 01/17/2023] Open
Abstract
In marine ecosystems, most invertebrates possess diverse microbiomes on their external surfaces, such as those found in the pedal mucus of grazing gastropods and chitons that aids displacement on different surfaces. The microbes are then transported around and placed in contact with free-living microbial communities of micro and other macro-organisms, potentially exchanging species and homogenizing microbial composition and structure among grazer hosts. Here, we characterize the microbiota of the pedal mucus of five distantly related mollusk grazers, quantify differences in microbial community structure, mucus protein and carbohydrate content, and, through a simple laboratory experiment, assess their effects on integrated measures of biofilm abundance. Over 665 Amplicon Sequence Variants (ASVs) were found across grazers, with significant differences in abundance and composition among grazer species and epilithic biofilms. The pulmonate limpet Siphonaria lessonii and the periwinkle Echinolittorina peruviana shared similar microbiota. The microbiota of the chiton Chiton granosus, keyhole limpet Fissurella crassa, and scurrinid limpet Scurria araucana differed markedly from one another, and form those of the pulmonate limpet and periwinkle. Flavobacteriaceae (Bacteroidia) and Colwelliaceae (Gammaproteobacteria) were the most common among microbial taxa. Microbial strict specialists were found in only one grazer species. The pedal mucus pH was similar among grazers, but carbohydrate and protein concentrations differed significantly. Yet, differences in mucus composition were not reflected in microbial community structure. Only the pedal mucus of F. crassa and S. lessonii negatively affected the abundance of photosynthetic microorganisms in the biofilm, demonstrating the specificity of the pedal mucus effects on biofilm communities. Thus, the pedal mucus microbiota are distinct among grazer hosts and can affect and interact non-trophically with the epilithic biofilms on which grazers feed, potentially leading to microbial community coalescence mediated by grazer movement. Further studies are needed to unravel the myriad of non-trophic interactions and their reciprocal impacts between macro- and microbial communities.
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Affiliation(s)
- Clara Arboleda-Baena
- Estación Costera de Investigaciones Marinas and Center for Applied Ecology and Sustainability (CAPES), Pontificia Universidad Católica de Chile, El Tabo, Chile,Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago de Chile, Región Metropolitana, Chile
| | - Claudia Belén Pareja
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago de Chile, Región Metropolitana, Chile
| | - Isadora Pla
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago de Chile, Región Metropolitana, Chile
| | - Ramiro Logares
- Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalonia, Spain
| | - Rodrigo De la Iglesia
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago de Chile, Región Metropolitana, Chile,Marine Energy Research & Innovation Center (MERIC), Santiago de Chile, Chile
| | - Sergio Andrés Navarrete
- Estación Costera de Investigaciones Marinas and Center for Applied Ecology and Sustainability (CAPES), Pontificia Universidad Católica de Chile, El Tabo, Chile,Marine Energy Research & Innovation Center (MERIC), Santiago de Chile, Chile,Centro Basal COPAS-COASTAL, Universidad de Concepción
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Xu Z, Hou Y, Sun J, Zhu L, Zhang Q, Yao W, Fan X, Zhang K, Piao JG, Wei Y. Deoxycholic acid-chitosan coated liposomes combined with in situ colonic gel enhances renal fibrosis therapy of emodin. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2022; 101:154110. [PMID: 35487039 DOI: 10.1016/j.phymed.2022.154110] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/30/2022] [Accepted: 04/14/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Renal fibrosis is the final common pathological feature of various chronic kidney diseases (CKD). Despite recent advances, development of new treatments strategy is needed. Emodin (EMO), an important ingredient of Chinese medicine, rhubarb (Polygonaceae Rheum palmatum l.), has been reported to inhibit the development of renal fibrosis effectively. However, the poor oral bioavailability of EMO and the insufficient monotherapy therapy compromise its efficacy. PURPOSE In order to enhance renal fibrosis therapy of emodin, an innovative combination therapy based on deoxycholic acid-chitosan coated liposomes (DCS-Lips) and in situ colonic gel (IGE) was developed. METHODS For one, the DCS-Lips were prepared via electrostatic interaction by mixing anionic conventional Lips with cationic DCS, deoxycholic acid conjugated on the backbone of chitosan. The cellular uptake of FITC-labeled DCS-Lips in Caco-2 cell monolayer was evaluated by CLSM and flow cytometry, respectively. Permeability study was carried out using Caco-2 cell monolayer. For another, EMO-loaded in situ colonic gel (EMO-IGE) was prepared by mixing EMO nanosuspensions and plain in situ gel, which was obtained by the cold method. The EMO-IGE was assessed for morphology, gelation temperature, viscosity and in vitro drug release. Finally, the therapeutic efficacy of the combination strategy, oral DCS-Lips formulations and in situ colonic gel, was evaluated in unilateral ureteral obstruction (UUO) rat model. Additionally, 16S rDNA sequencing was performed on rats faces to investigate whether the combination strategy improves the microbial dysbiosis in UUO rats. RESULTS The prepared DCS-Lips produced small, uniformly sized nanoparticles, and significantly enhanced the cellular uptake and in vitro permeability of EMO compared to non-coated liposomes. Moreover, the EMO-IGE was characterized by short gelation time, optimal gelling temperature, and excellent viscosity. In UUO model, the combination of DCS-Lips (gavage) and IGE (enema) attenuated renal fibrosis effectively. The results of 16S rDNA sequencing illustrated that IGE could restore the gut microbial dysbiosis of UUO rats. CONCLUSION Overall, the combination of DCS-Lips and EMO-IGE alleviated renal fibrosis effectively, resulting from the improved oral bioavailability of EMO by DCS-Lips and the restoration of gut microbiota by EMO-IGE, thus, presenting an innovative and promising potential for renal fibrosis treatment.
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Affiliation(s)
- Zhishi Xu
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 311402, China
| | - Yu Hou
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 311402, China
| | - Jiang Sun
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 311402, China
| | - Lin Zhu
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 311402, China
| | - Qibin Zhang
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 311402, China
| | - Wenjie Yao
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 311402, China
| | - Xudong Fan
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 311402, China
| | - Ke Zhang
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 311402, China
| | - Ji-Gang Piao
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 311402, China
| | - Yinghui Wei
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 311402, China.
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