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Lv A, BianBaZhuoMa, DeQiong, DaWaZhuoMa, PuBuZhuoMa, Yao D, LangJiQuZhen, Lu Y, Cai L, DaZhen, Tang C, BianBaZhuoMa, Zhang Y, Yin J, Ding T, DaWaCang, Wu M, Chen Y, Li Y. Effect of COVID-19 infection on pregnant women in plateau regions. Public Health 2024; 229:57-62. [PMID: 38401193 DOI: 10.1016/j.puhe.2023.12.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 12/04/2023] [Accepted: 12/28/2023] [Indexed: 02/26/2024]
Abstract
OBJECTIVE The present study aims to explore the effect of COVID-19 infection on pregnant women in plateau regions. STUDY DESIGN Data from 381 pregnant women infected with COVID-19 who underwent prenatal examination or treatment at Women and Children's Hospital of Tibet Autonomous Region between January 2020 and December 2022 and 314 pregnant women not infected with COVID-19 were retrospectively collected. METHODS The study participants were divided into an infected and non-infected group according to whether they were infected with COVID-19. Basic information (ethnicity, age, body mass index and gestational age [GA]), vaccination status, intensive care unit (ICU) admission and delivery outcomes were compared. Binary logistic regression was used to analyse the influencing factors of ICU admission. RESULTS The results revealed significant differences in the GA, vaccination rate, blood pressure, partial pressure of oxygen, white blood cell (WBC) count, ICU admission rate, preeclampsia rate, forearm presentation rate, thrombocytopenia rate, syphilis infection rate and placental abruption rate between the two groups (P < 0.05). A univariate analysis showed that COVID-19 infection, hepatitis B virus infection, the WBC count and hypoproteinaemia were risk factors for ICU admission. The results of the multivariate analysis of the ICU admission of pregnant women showed that COVID-19 infection (odds ratio [OR] = 4.271, 95 % confidence interval [CI]: 3.572-5.820, P < 0.05) was a risk factor for ICU admission and the WBC count (OR = 0.935, 95 % CI: 0.874-0.947, P < 0.05) was a protective factor for ICU admission. CONCLUSION Pregnant women are vulnerable to the adverse consequences of COVID-19 infection, and public health measures such as vaccination are needed to protect this population subgroup.
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Affiliation(s)
- A Lv
- Department of Obstetrics and Gynecology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, NO. 1 DaHua Road, Dong Dan, Beijing, 100730, PR China; Women and Children's Hospital of Tibet Autonomous Region, NO. 10 Chagu Avenue, Doilungdêqên District, Liuwu New Area, Lhasa, Tibet Autonomous Region, 851414, PR China
| | - BianBaZhuoMa
- Lhasa People's Hospital, No. 1, Beijing Middle Road, Chengguan District, Lhasa, Tibet Autonomous Region, 850000, PR China
| | - DeQiong
- Women and Children's Hospital of Tibet Autonomous Region, NO. 10 Chagu Avenue, Doilungdêqên District, Liuwu New Area, Lhasa, Tibet Autonomous Region, 851414, PR China
| | - DaWaZhuoMa
- Women and Children's Hospital of Tibet Autonomous Region, NO. 10 Chagu Avenue, Doilungdêqên District, Liuwu New Area, Lhasa, Tibet Autonomous Region, 851414, PR China
| | - PuBuZhuoMa
- Lhasa People's Hospital, No. 1, Beijing Middle Road, Chengguan District, Lhasa, Tibet Autonomous Region, 850000, PR China
| | - D Yao
- Nyingchi People's Hospital, No. 11, Water Garden, Bayi Town, Bayi District, Nyingchi City, Tibet Autonomous Region, 860000, PR China
| | - LangJiQuZhen
- Women and Children's Hospital of Tibet Autonomous Region, NO. 10 Chagu Avenue, Doilungdêqên District, Liuwu New Area, Lhasa, Tibet Autonomous Region, 851414, PR China
| | - Y Lu
- Women and Children's Hospital of Tibet Autonomous Region, NO. 10 Chagu Avenue, Doilungdêqên District, Liuwu New Area, Lhasa, Tibet Autonomous Region, 851414, PR China
| | - L Cai
- Women and Children's Hospital of Tibet Autonomous Region, NO. 10 Chagu Avenue, Doilungdêqên District, Liuwu New Area, Lhasa, Tibet Autonomous Region, 851414, PR China
| | - DaZhen
- Women and Children's Hospital of Tibet Autonomous Region, NO. 10 Chagu Avenue, Doilungdêqên District, Liuwu New Area, Lhasa, Tibet Autonomous Region, 851414, PR China
| | - C Tang
- Women and Children's Hospital of Tibet Autonomous Region, NO. 10 Chagu Avenue, Doilungdêqên District, Liuwu New Area, Lhasa, Tibet Autonomous Region, 851414, PR China
| | - BianBaZhuoMa
- Women and Children's Hospital of Tibet Autonomous Region, NO. 10 Chagu Avenue, Doilungdêqên District, Liuwu New Area, Lhasa, Tibet Autonomous Region, 851414, PR China
| | - Y Zhang
- Women and Children's Hospital of Tibet Autonomous Region, NO. 10 Chagu Avenue, Doilungdêqên District, Liuwu New Area, Lhasa, Tibet Autonomous Region, 851414, PR China
| | - J Yin
- Women and Children's Hospital of Tibet Autonomous Region, NO. 10 Chagu Avenue, Doilungdêqên District, Liuwu New Area, Lhasa, Tibet Autonomous Region, 851414, PR China
| | - T Ding
- Women and Children's Hospital of Tibet Autonomous Region, NO. 10 Chagu Avenue, Doilungdêqên District, Liuwu New Area, Lhasa, Tibet Autonomous Region, 851414, PR China
| | - DaWaCang
- Tibet University Medical School, No. 10, Zangda East Road, Chengguan District, Lhasa, Tibet Autonomous Region, 850000, PR China
| | - M Wu
- Tibet University Medical School, No. 10, Zangda East Road, Chengguan District, Lhasa, Tibet Autonomous Region, 850000, PR China
| | - Y Chen
- Tibet University Medical School, No. 10, Zangda East Road, Chengguan District, Lhasa, Tibet Autonomous Region, 850000, PR China
| | - Y Li
- Department of Obstetrics and Gynecology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, NO. 1 DaHua Road, Dong Dan, Beijing, 100730, PR China.
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Huo J, Li X, Hu X, Lv A. Multi-omics analysis of miRNA-mediated intestinal microflora changes in crucian carp Carassius auratus infected with Rahnella aquatilis. Front Immunol 2024; 15:1335602. [PMID: 38426108 PMCID: PMC10902443 DOI: 10.3389/fimmu.2024.1335602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/19/2024] [Indexed: 03/02/2024] Open
Abstract
Infection by an emerging bacterial pathogen Rahnella aquatilis caused enteritis and septicemia in fish. However, the molecular pathogenesis of enteritis induced by R. aquatilis infection and its interacting mechanism of the intestinal microflora associated with microRNA (miRNA) immune regulation in crucian carp Carassius auratus are still unclear. In this study, C. auratus intraperitoneally injected with R. aquatilis KCL-5 was used as an experimental animal model, and the intestinal pathological changes, microflora, and differentially expressed miRNAs (DEMs) were investigated by multi-omics analysis. The significant changes in histopathological features, apoptotic cells, and enzyme activities (e.g., lysozyme (LYS), alkaline phosphatase (AKP), alanine aminotransferase (ALT), aspartate transaminase (AST), and glutathione peroxidase (GSH-Px)) in the intestine were examined after infection. Diversity and composition analysis of the intestinal microflora clearly demonstrated four dominant bacteria: Proteobacteria, Fusobacteria, Bacteroidetes, and Firmicutes. A total of 87 DEMs were significantly screened, and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the potential target genes were mainly involved in the regulation of lipid, glutathione, cytosine, and purine metabolism, which participated in the local immune response through the intestinal immune network for IgA production, lysosome, and Toll-like receptor (TLR) pathways. Moreover, the expression levels of 11 target genes (e.g., TLR3, MyD88, NF-κB, TGF-β, TNF-α, MHC II, IL-22, LysC, F2, F5, and C3) related to inflammation and immunity were verified by qRT-PCR detection. The correlation analysis indicated that the abundance of intestinal Firmicutes and Proteobacteria was significantly associated with the high local expression of miR-203/NF-κB, miR-129/TNF-α, and miR-205/TGF-β. These findings will help to elucidate the molecular regulation mechanism of the intestinal microflora, inflammation, and immune response-mediated miRNA-target gene axis in cyprinid fish.
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Affiliation(s)
- Jiaxin Huo
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, China
| | - Xiaowei Li
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, China
| | - Xiucai Hu
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, China
| | - Aijun Lv
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, China
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Huo Y, Hu X, Lü J, Luo F, Liang J, Lei H, Lv A. Single-cell transcriptome, phagocytic activity and immunohistochemical analysis of crucian carp (Carassius auratus) in response to Rahnella aquatilis infection. Fish Shellfish Immunol 2023; 140:108970. [PMID: 37488042 DOI: 10.1016/j.fsi.2023.108970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/14/2023] [Accepted: 07/20/2023] [Indexed: 07/26/2023]
Abstract
In teleost fish, kidney is an important immune and hematopoietic organ with multiple physiological functions. However, the immune cells and cellular markers of kidney require further elucidation in crucian carp (C. auratus). Here we report on the single-cell transcriptional landscape in posterior kidney, immunohistochemical and phagocytic features of C. auratus with R. aquatilis infection. The results showed that a total of 18 cell populations were identified for the main immune cells such as monocytes/macrophages (Mo/Mφ), dendritic cells (DCs), B cells, T cells, granulocytes and hematopoietic progenitor cells (HPCs). Pseudo-time trajectory analysis was reconstructed for the immune cells using Monocle2 to obtain additional insights into their developmental lineage relationships. In the detected tissues (liver, spleen, kidney, intestine, skin, and gills) of infected fish exhibited positive immunohistochemical staining with prepared for antibody to R. aquatilis. Apoptotic cells were fluorescently demonstrated by TUNEL assay, and bacterial phagocytic activity were observed for neutrophils and Mo/Mφ cells, respectively. Moreover, a similar up-ward/down-ward expression trend of the selected immune and inflammatory genes was found in the kidney against R. aquatilis infection, which were significantly involved in TLR/NLR, ECM adhesion, phago-lysosome, apoptosis, complement and coagulation pathways. To our knowledge, this is the first report on the detailed characterization of immune cells and host-R. aquatilis interaction, which will contribute to understanding on the biology of renal immune cells and repertoire of potential markers in cyprinid fish species.
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Affiliation(s)
- Yian Huo
- College of Fisheries, Tianjin Agricultural University, Tianjin, 300392, China
| | - Xiucai Hu
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, Tianjin Agricultural University, Tianjin, 300392, China
| | - Jiarui Lü
- School of Foreign Languages, Peking University, Beijing, 100871, China
| | - Fuli Luo
- College of Fisheries, Tianjin Agricultural University, Tianjin, 300392, China
| | - Jing Liang
- College of Fisheries, Tianjin Agricultural University, Tianjin, 300392, China
| | - Haibo Lei
- College of Basic Science, Tianjin Agricultural University, Tianjin, 300392, China
| | - Aijun Lv
- College of Fisheries, Tianjin Agricultural University, Tianjin, 300392, China; Tianjin Key Lab of Aqua-Ecology and Aquaculture, Tianjin Agricultural University, Tianjin, 300392, China.
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Liu H, Hu X, Lian Z, Luo Z, Lv A, Tan J. Focal adhesion signaling pathway involved in skin immune response of tongue sole Cynoglossus semilaevis to Vibrio vulnificus infection. Fish Shellfish Immunol 2023; 135:108651. [PMID: 36863497 DOI: 10.1016/j.fsi.2023.108651] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 02/24/2023] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
Focal adhesion (FA) plays a key role in cell adhesion, migration and antibacterial immune, but it remained unclear in fish. In this study, half-smooth tongue sole Cynoglossus semilaevis were infected with Vibrio vulnificus, and then immune-related protein in the skin, especially for FA signaling pathway were screened and identified by iTRAQ analysis. Results showed that the differentially expressed proteins (DEPs) in skin immune response (eg., ITGA6, FN, COCH, AMBP, COL6A1, COL6A3, COL6A6, LAMB1, LAMC1, FLMNA) were firstly found in FA signaling pathway. Furthermore, the validation analysis of FA-related genes were basically consistent with the iTRAQ data at 36 hpi (r = 0.678, p < 0.01), and their spatio-temporal expressions were confirmed by qPCR analysis. The molecular characterization of vinculin of C. semilaevis was described. This study will provide a new perspective for understanding the molecular mechanism of FA signaling pathway in the skin immune response in marine fish.
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Affiliation(s)
- Houfu Liu
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, 300384, China
| | - Xiucai Hu
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, 300384, China
| | - Zhengyi Lian
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, 300384, China
| | - Zhang Luo
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, 300384, China
| | - Aijun Lv
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, 300384, China.
| | - Jing Tan
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, 300384, China
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Huo J, Hu X, Bai J, Lv A. Multiomics analysis revealed miRNAs as potential regulators of the immune response in Carassius auratus gills to Aeromonas hydrophila infection. Front Immunol 2023; 14:1098455. [PMID: 36820086 PMCID: PMC9938762 DOI: 10.3389/fimmu.2023.1098455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/11/2023] [Indexed: 02/06/2023] Open
Abstract
The gill of fish is an important immune organ for pathogen defense, but its microRNA (miRNA) expression and regulatory mechanism remain unclear. In this study, we report on the histopathological and immunohistochemical features of the gills of the crucian carp Carassius auratus challenged with Aeromonas hydrophila. Small RNA libraries of the gills were constructed and sequenced on the Illumina HiSeq 2000 platform. A total of 1,165 differentially expressed miRNAs (DEMs) were identified in gills, of which 539 known and 7 unknown DEMs were significantly screened (p < 0.05). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the potential target genes/proteins were primarily involved in 33 immune-related pathways, in which the inflammatory responses were focused on the Toll-like receptor (TLR), mitogen-activated protein kinase (MAPK), and nuclear factor kappa B (NF-κB) signaling pathways. Moreover, the expression levels of 14 key miRNAs (e.g., miR-10, miR-17, miR-26a, miR-144, miR-145, and miR-146a) and their target genes (e.g., TNFα, TLR4, NF-κB, TAB1, PI3K, and IRAK1) were verified. In addition, the protein levels based on isobaric tags for relative and absolute quantification (iTRAQ) were significantly associated with the results of the quantitative real-time PCR (qRT-PCR) analysis (p < 0.01). miR-17/pre-miR-17 were identified in the regulation expression of the NF-κB target gene, and the phylogenetic tree analysis showed that the pre-miR-17 of C. auratus with the closest similarity to the zebrafish Danio rerio is highly conserved in teleosts. This is the first report of the multi-omics analysis of the miRNAs and proteins in the gills of C. auratus infected with A. hydrophila, thus enriching knowledge on the regulation mechanism of the local immune response in Cyprinidae fish.
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Affiliation(s)
- Jiaxin Huo
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, China
| | - Xiucai Hu
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, China
| | - Jie Bai
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, China
| | - Aijun Lv
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, China
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Liu H, Xu X, Bai X, Li Y, Wang J, Lv A, Luo Z. Development of a TaqMan real-time quantitative PCR assay to detect Metschnikowia bicuspidata in Chinese mitten crab Eriocheir sinensis. Dis Aquat Organ 2022; 152:17-25. [PMID: 36394137 DOI: 10.3354/dao03704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Milky disease of Chinese mitten crab Eriocheir sinensis caused by Metschnikowia bicuspidata is a novel disease with high mortality. No effective treatment is currently available, but a rapid, accurate detection method is required for the prevention and control of the disease. In this study, the genome-sequencing results of M. bicuspidata and similar species were used for comparative genomic analysis for genes specific to M. bicuspidata. A quantitative PCR (qPCR) detection method for M. bicuspidata was then established using the specific primers and probes designed according to the sequence of a hypothetical protein gene specific to M. bicuspidata. The assay was found to have a high degree of repeatability and reproducibility, with a linear dynamic range (R2 = 0.998) extending over 9 log10 dilutions and a high efficiency (100.7%). Furthermore, the method showed high sensitivity, being able to detect at least 11.3 copies μl-1 of recombinant plasmid, and strong specificity, without any cross-reaction with any of the 9 species of yeast that are closely related to M. bicuspidata or any of 16 species of pathogenic bacteria commonly observed in aquatic animals. The established method was used to examine 138 apparently healthy crabs collected from 22 farms, with 21 samples (15.2%) found to be M. bicuspidata-positive. Thus, the developed qPCR assay is a specific, sensitive, stable, and rapid diagnostic method for the detection and quantification of M. bicuspidata DNA from E. sinensis tissues.
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Affiliation(s)
- Houfu Liu
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, PR China
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Li X, Hu X, Lv A, Guan Z. Skin immune response to Aeromonas hydrophila infection in crucian carp Carassius auratus revealed by multi-omics analysis. Fish Shellfish Immunol 2022; 127:866-875. [PMID: 35850458 DOI: 10.1016/j.fsi.2022.07.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/13/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Fish skin is an essential protective barrier and functions as the first line of immune defense against pathogens. However, the molecular mechanism at the proteome-level remains unclear in the skin of fish. In this study, the comparative proteomics of skin immune responses of crucian carp Carassius auratus infected with Aeromonas hydrophila was investigated by isobaric tags for relative and absolute quantification (iTRAQ), two-dimensional gel electrophoresis combined with mass spectrometry (2-DE/MS) as well as high-throughput transcriptome (RNA-seq) techniques. A total of 241 and 178 differentially expressed proteins (DEPs) at 6 and 12 h post-infection (hpi) were respectively identified by iTRAQ, and key-DEPs were furtherly verified with 2-DE/MS analysis. GO and KEGG analysis showed that these DEPs were mostly related to metabolism, regulation of the cytoskeleton, stress and immune responses. Co-association results of proteome and transcriptome revealed the lysozyme (LYZ), complement C3, DnaJ (Hsp40) homolog subfamily C member 8 (DNAJC8) and allograft inflammatory factor 1-like (AIF1L) play important roles in skin immune responses of crucian carp. The significantly up-regulated expression of detected immune-related genes (c3, mapk3, f5, nlr, hsp90, itgb2, fnl, flnca, p47, mhc and pros1) were validated by qRT-PCR analysis. To our knowledge, this is first report on multi-omics analysis of the differential proteomics for the skin immune response of C. auratus against A.hydrophila infection, which contribute to the understanding the mechanisms of skin mucosal immunity in cyprinid fish.
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Affiliation(s)
- Xiaowei Li
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, 300384, China
| | - Xiucai Hu
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, 300384, China
| | - Aijun Lv
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, 300384, China.
| | - Zhenguo Guan
- S&E Burgeoning Biotechnology (Tianjin) Co., Ltd, Tianjin, 300383, China
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Zhang X, Sun J, Zhu Y, Han Z, Hu X, Lv A, Guo Y. First record of isolation and characterization of Vibrio sinaloensis from diseased orange-spotted grouper Epinephelus coioides. Dis Aquat Organ 2022; 149:71-76. [PMID: 35608511 DOI: 10.3354/dao03665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A dominant bacterium, ZYL-12, isolated from the liver of a diseased orange-spotted grouper Epinephelus coioides, was identified as Vibrio sinaloensis, based on phenotypic and molecular analysis. The median lethal dosage of ZYL-12 was calculated as 1.6 × 105 CFU g-1 fish weight. The infection experiment indicated that ZYL-12 caused noticeable histological lesions to the liver, kidney and spleen of the fish. Growth characteristics showed that ZYL-12 possessed strong environmental adaptability. This note is the first report about the pathogenicity of V. sinaloensis isolated from diseased fish.
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Affiliation(s)
- Xue Zhang
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin 300380, PR China
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Zhang X, Sun J, Chen F, Qi H, Chen L, Sung YY, Huang Y, Lv A, Hu X. Phenotypic and genomic characterization of a Vibrio parahaemolyticus strain causing disease in Penaeus vannamei provides insights into its niche adaptation and pathogenic mechanism. Microb Genom 2021; 7. [PMID: 33952389 PMCID: PMC8209731 DOI: 10.1099/mgen.0.000549] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The virulence of Vibrio parahaemolyticus is variable depending on its virulence determinants. A V. parahaemolyticus strain, in which the virulence is governed by the pirA and pirB genes, can cause acute hepatopancreatic necrosis disease (AHPND) in shrimps. Some V. parahaemolyticus that are non-AHPND strains also cause shrimp diseases and result in huge economic losses, while their pathogenicity and pathogenesis remain unclear. In this study, a non-AHPND V. parahaemolyticus, TJA114, was isolated from diseased Penaeus vannamei associated with a high mortality. To understand its virulence and adaptation to the external environment, whole-genome sequencing of this isolate was conducted, and its phenotypic profiles including pathogenicity, growth characteristics and nutritional requirements were investigated. Shrimps following artificial infection with this isolate presented similar clinical symptoms to the naturally diseased ones and generated obvious pathological lesions. The growth characteristics indicated that the isolate TJA114 could grow well under different salinity (10–55 p.p.t.), temperature (23–37 °C) and pH (6–10) conditions. Phenotype MicroArray results showed that this isolate could utilize a variety of carbon sources, amino acids and a range of substrates to help itself adapt to the high hyperosmotic and alkaline environments. Antimicrobial-susceptibility test showed that it was a multidrug-resistant bacterium. The whole-genomic analysis showed that this V. parahaemolyticus possessed many important functional genes associated with multidrug resistance, stress response, adhesions, haemolysis, putative secreted proteases, dedicated protein secretion systems and a variety of nutritional metabolic mechanisms. These annotated functional genes were confirmed by the phenotypic profiles. The results in this study indicated that this V. parahaemolyticus isolate possesses a high pathogenicity and strong environmental adaptability.
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Affiliation(s)
- Xue Zhang
- Tianjin Key Laboratory of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin 300384, PR China
| | - Jingfeng Sun
- Tianjin Key Laboratory of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin 300384, PR China
| | - Feng Chen
- Tianjin Key Laboratory of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin 300384, PR China
| | - Hongli Qi
- Tianjin Key Laboratory of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin 300384, PR China
| | - Limei Chen
- Tianjin Key Laboratory of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin 300384, PR China
| | - Yeong Yik Sung
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu 21030, Malaysia
| | - Yadong Huang
- Tianjin Hengqian Aquaculture Co. Ltd, Tianjin 300270, PR China
| | - Aijun Lv
- Tianjin Key Laboratory of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin 300384, PR China
| | - Xiucai Hu
- Tianjin Key Laboratory of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin 300384, PR China
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Han Z, Sun J, Wang A, Lv A, Hu X, Chen L, Guo Y. Differentially expressed proteins in the intestine of Cynoglossus semilaevis Günther following a Shewanella algae challenge. Fish Shellfish Immunol 2020; 104:111-122. [PMID: 32525078 DOI: 10.1016/j.fsi.2020.06.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 05/31/2020] [Accepted: 06/06/2020] [Indexed: 06/11/2023]
Abstract
Fish intestine is an important constituent of the mucosal immune system. The gut and gut-associated lymphoid tissue construct a local immune environment. A Shewanella algae strain was previously reported to be a pathogen causing ascitic disease accompanied with intestinal inflammation in Cynoglossus semilaevis. This study aimed to investigate the intestine immune response in C. semilaevis to S. algae infection at the protein level. Two-dimensional electrophoresis coupled with mass spectrometry proteomics was utilized to compare protein expression in the intestines from normal and S. algae-infected C. semilaevis. A total of 70 differentially expressed proteins (DEPs), consisting of 16 upregulated and 54 downregulated proteins, were identified in the intestine tissue of C. Semilaevis. These protein expression changes were further validated using western blot analysis and quantitative real-time PCR. Gene ontology enrichment analysis showed that these 70 DEPs could be assigned across three categories: "cellular components", "molecular function", and "biological process". Forty-one DEPs (six up-regulated and 35 down-regulated proteins) related to metabolic processes were identified. In addition, 20 DEPs (eight up-regulated and 12 down-regulated proteins) related to stress and immune responses were identified. A protein-protein interaction network generated by the STRING (Search Tool for the Retrieval of Interacting Genes/protein) revealed that 30 DEPs interacted with one another to form an integrated network. Among them, 29 DEPs were related to stress, immune, and metabolism processes. In the network, some of the immune related proteins (C9, FGB, KNG1, apolipoprotein A-IV-like, and PDIA3) were up-regulated and most DEPs involved in metabolism processes were down-regulated. These results indicate that the immune defense response of the intestine was activated and the intestinal function associated with metabolism processes was disturbed. This study provides valuable information for further research into the functions of these DEPs in fish.
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Affiliation(s)
- Zhuoran Han
- Key Laboratory of Ecology and Environment Science of Higher Education Institutes, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, College of Life Science, South China Normal University, Guangzhou, 510631, China; Tianjin Key Laboratory of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, 300384, China.
| | - Jingfeng Sun
- Tianjin Key Laboratory of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, 300384, China.
| | - Anli Wang
- Key Laboratory of Ecology and Environment Science of Higher Education Institutes, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, College of Life Science, South China Normal University, Guangzhou, 510631, China.
| | - Aijun Lv
- Tianjin Key Laboratory of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, 300384, China.
| | - Xiucai Hu
- Tianjin Key Laboratory of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, 300384, China.
| | - Limei Chen
- Tianjin Key Laboratory of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, 300384, China.
| | - Yongjun Guo
- Tianjin Key Laboratory of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, 300384, China.
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11
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Chen F, Sun J, Han Z, Yang X, Xian JA, Lv A, Hu X, Shi H. Isolation, Identification and Characteristics of Aeromonas veronii From Diseased Crucian Carp ( Carassius auratus gibelio). Front Microbiol 2019; 10:2742. [PMID: 32038507 PMCID: PMC6988821 DOI: 10.3389/fmicb.2019.02742] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 11/11/2019] [Indexed: 11/13/2022] Open
Abstract
Aeromonas species often cause disease in farmed fish. In the present study, dominant bacteria were isolated from diseased crucian carp (Carassius auratus gibelio). Based on this, a bacterial isolate was tentatively named CFJY-623. This isolate was identified as Aeromonas veronii based on analysis of its morphological, physiological, and biochemical features, as well as 16S rRNA and gyrB gene sequences. Six virulence genes related to pathogenicity including aerolysin, cytotonic enterotoxins, elastase, glycerophospholipid: cholesterol acyltransferase, lipase, and serine protease were identified in this A. veronii isolate. The median lethal dosage (LD50) of the CFJY-623 isolate for crucian carp was determined as 1.31 × 107 CFU/mL. Artificial experimental infection showed that the CFJY-623 isolate caused considerable histological lesions in the fish, including tissue cell degeneration, necrosis, and inflammatory cell infiltrating. Drug sensitivity testing showed that the isolate was susceptible to aminoglycosides, carbapenemes, and nitrofurans. Exploring its growing features showed that this isolate exhibited a high level of environmental adaptability. These results provided a scientific basis for the identification of A. veronii and treatment for fish infected by this pathogen.
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Affiliation(s)
- Feng Chen
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, China
| | - Jingfeng Sun
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, China
| | - Zhuoran Han
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, China
| | - Xijun Yang
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, China
| | - Jian-an Xian
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Aijun Lv
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, China
| | - Xiucai Hu
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, China
| | - Hongyue Shi
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, China
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12
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Sun J, Wang Y, Lv A, Xian JA, Wang Q, Zhang S, Guo Y, Xing K. Histochemical distribution of four types of enzymes and mucous cells in the intestine of koi carp (Cyprinus carpio var. koi). Fish Physiol Biochem 2019; 45:1367-1376. [PMID: 31209688 DOI: 10.1007/s10695-019-00673-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 06/09/2019] [Indexed: 06/09/2023]
Abstract
The main purpose of this study was to investigate the distribution of acid phosphatase (ACP), alkaline phosphatase (ALP), non-specific esterase (NSE), peroxidase (POD), and mucous cells in the intestine of the koi carp Cyprinus carpio var. koi. ACP activity was located in the striated border, enterocytes, and lamina propria of the anterior and middle intestines. The ACP activity in the anterior intestine was higher than that in the middle and posterior intestines. ALP existed in the striated border of enterocytes and lamina propria, serosa, muscular layer, and the junction between muscular layer and submucosa layer of the intestine. The ALP activity in the anterior intestine was higher than that in the middle and posterior intestines. NSE activity was localized in the cytoplasm of enterocytes in the whole intestine, and the middle intestine showed the lower NSE activity than the anterior and posterior intestines. POD activity was localized in the blood cells of the lamina propria and cytoplasm of enterocytes in all intestinal segments. The POD activity among the anterior, middle, and posterior intestines was non-significantly different. Alcian blue periodic acid-Schiff histochemical results revealed three types of mucous cells in the intestine. The total number of mucous cells and percentage of type I cells among the anterior, middle, and posterior intestines were non-significantly different. The percentage of the type II cells was the highest in the posterior intestine, while the lowest in the anterior intestine. The percentage of the type III cells was the highest in the anterior intestine, while the lowest in the posterior intestine.
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Affiliation(s)
- Jingfeng Sun
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, 300384, China.
| | - Yize Wang
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, 300384, China
| | - Aijun Lv
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, 300384, China
| | - Jian-An Xian
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Qingkui Wang
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, 300384, China
| | - Shulin Zhang
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, 300384, China
| | - Yongjun Guo
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, 300384, China
| | - Kezhi Xing
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, 300384, China
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13
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Jiang B, Sun J, Lv A, Hu X, Shi H, Sung Y, Wang Q, Wang Y. Impact of DNA extraction methods on the observed microbial communities from the intestinal flora of the penaeid shrimp Litopenaeus vannamei. FEMS Microbiol Lett 2019; 366:5487890. [PMID: 31074797 DOI: 10.1093/femsle/fnz099] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 05/09/2019] [Indexed: 12/25/2022] Open
Abstract
Two DNA extraction methods, the Zirmil-beating cell disruption method (ZBC) and the QIAamp fast DNA stool mini kit (QIA), were used to extract DNA from the intestinal flora of the penaeid shrimp Litopenaeus vannamei, and their microbial communities were analyzed using 16S rDNA high-throughput sequencing. Results were obtained in terms of the number of reads, alpha diversity indexes, beta diversity indexes and taxonomic composition. The alpha diversity indexes of the community, according to the ZBC method, were higher than those according to the QIA method. Furthermore, results from the three samples using the ZBC method were less consistent than those where the QIA method was used. Further, using the latter method led to substantive clustering. It is suggested that the QIA method is more stable and repeatable than the ZBC method. Although the two extraction methods shared the major abundant microflora based on 16S rDNA high-throughput sequencing, bias associated with diversity analysis indexes and certain species was observed.
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Affiliation(s)
- Boyun Jiang
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China
| | - Jingfeng Sun
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China
| | - Aijun Lv
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China
| | - Xiucai Hu
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China
| | - Hongyue Shi
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China
| | - YeongYik Sung
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China.,Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Terengganu 21030, Malaysia
| | - Qingkui Wang
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China
| | - Yang Wang
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China
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Li Z, Wang X, Chen C, Gao J, Lv A. Transcriptome profiles in the spleen of African catfish (Clarias gariepinus) challenged with Aeromonas veronii. Fish Shellfish Immunol 2019; 86:858-867. [PMID: 30572129 DOI: 10.1016/j.fsi.2018.12.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 12/10/2018] [Accepted: 12/15/2018] [Indexed: 06/09/2023]
Abstract
The African catfish, Clarias gariepinus, an important cultured freshwater species in many countries, possess the characteristic of high disease resistance. However, little genomic information for this character of the fish is available up to now. To address the shortfall and to better understand C. gariepinus immune response to pathogen infection at molecular level, C. gariepinus were challenged with potent A. veronii and the high-throughput RNA sequencing (RNA-seq) technology were employed to produce transcriptomes from spleen. In total, an average of 46,073,372 clean reads obtained were de novo assembled into 156,955 unigenes with an average length of 1082 bp. All of unigenes were annotated to seven public databases. Three comparisons were separately conducted between the infected groups at 3 h, 24 h, 48 h post-challenge and control group. A total of 2482 differentially expressed unigenes (DEGs) were identified. Among these, 114 immune-related DEGs were captured, including 88, 42, and 31 genes at 3 h, 24 h and 48 h after infection respectively, for analysis of expression pattern and enrichment. The 114 DEGs displayed four expression patterns by cluster analysis and they were significantly enriched in 38 pathways (q < 0.01) related to the immune or disease, five of which were NF-kappa B, TNF, NLR, TLR and RLR pathways. Finally, the expression levels of twelve selected immune-related DEGs involved in above five pathways were scrutinized. Seven of which were up-regulated at 3 h after infection, afterward, their expression dropped to control level. In summary, this study provides valuable transcriptome resource for understanding the defense mechanisms of C. gariepinus in resistance to pathogens from the gene expression viewpoint, which also open up the possibility to study the immune complexity and to better comprehend the interrelationships between some immune pathways in C. gariepinus.
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Affiliation(s)
- Zhuanzhuan Li
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, 300384, China.
| | - Xiaomei Wang
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, 300384, China.
| | - Chengxun Chen
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, 300384, China.
| | - Jinwei Gao
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, 300384, China.
| | - Aijun Lv
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, 300384, China.
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15
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Han Z, Sun J, Lv A, Xian JA, Sung YY, Sun X, Hu X, Xing K. Transcriptome profiling of immune-responsive genes in the intestine of Cynoglossus semilaevis Günther challenged with Shewanella algae. Fish Shellfish Immunol 2018; 80:291-301. [PMID: 29886138 DOI: 10.1016/j.fsi.2018.06.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 05/26/2018] [Accepted: 06/06/2018] [Indexed: 06/08/2023]
Abstract
To better understand gene expression in the intestine after Shewanella algae infection and provide insights into its immune roles in the tongue sole, Cynoglossus semilaevis, sequencing-based high-throughput RNA analysis (RNA-Seq) for the intestines between the control group and 12 h post-injection group was performed. After assembly, there was an average of 23,957,159 raw sequencing reads, and 23,943,491 clean reads were obtained after filtering out low-quality reads. Then, 383 differentially expressed genes (DEGs) in the intestines in response to S. algae infection were identified. Subsequently, gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of the DEGs were conducted to further explore their functions. Among all of the pathways involved, sixteen pathways were related to the immune system, among which the complement and coagulation cascades pathway was the most prominent for immunity-related DEGs, followed by the leukocyte transendothelial migration pathway. Furthermore, the expression levels of twelve selected DEGs in the immune-related pathways were identified by quantitative real-time polymerase chain reaction, substantiating the reliability and reproducibility of the RNA-Seq results. In summary, this study represents an important genomic resource for understanding the potential immune role of the tongue sole intestine from the perspective of gene expression.
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Affiliation(s)
- Zhuoran Han
- Tianjin Key Lab of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, 300384, China.
| | - Jingfeng Sun
- Tianjin Key Lab of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, 300384, China.
| | - Aijun Lv
- Tianjin Key Lab of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, 300384, China.
| | - Jian-An Xian
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.
| | - Yeong Yik Sung
- Tianjin Key Lab of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, 300384, China; Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Terengganu, 21030, Malaysia.
| | - Xueliang Sun
- Tianjin Key Lab of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, 300384, China.
| | - Xiucai Hu
- Tianjin Key Lab of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, 300384, China.
| | - Kezhi Xing
- Tianjin Key Lab of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, 300384, China.
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Han Z, Sun J, Lv A, Wang A. Biases from different DNA extraction methods in intestine microbiome research based on 16S rDNA sequencing: a case in the koi carp, Cyprinus carpio var. Koi. Microbiologyopen 2018; 8:e00626. [PMID: 29667371 PMCID: PMC6341036 DOI: 10.1002/mbo3.626] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 12/31/2017] [Accepted: 01/29/2018] [Indexed: 11/26/2022] Open
Abstract
This study examined the technical bias associated with different DNA extraction methods used in microbiome research. Three methods were used to extract genomic DNA from the same intestinal microbiota sample that was taken from the koi carp Cyprinus carpio var. koi, after which their microbial diversity and community structure were investigated on the basis of a 16S rDNA high‐throughput sequencing analysis. Biased results were observed in relation to the number of reads, alpha diversity indexes and taxonomic composition among the three DNA extraction protocols. A total of 1,381 OTUs from the intestinal bacteria were obtained, with 852, 759, and 698 OTUs acquired, using the Lysozyme and Ultrasonic Lysis method, Zirmil‐beating Cell Disruption method, and a QIAamp Fast DNA Stool Mini Kit, respectively. Additionally, 336 OTUs were commonly acquired, using the three methods. The results showed that the alpha diversity indexes (Rarefaction, Shannon, and Chao1) of the community that were determined using the Lysozyme and Ultrasonic Lysis method were higher than those obtained with the Zirmil‐beating Cell Disruption method, while the Zirmil method results were higher than those measured, using the QIAamp Fast DNA Stool Mini Kit. Moreover, all the major phyla (ratio>1%) could be identified with all three DNA extraction methods, but the phyla present at a lower abundance (ratio <1%) could not. Similar findings were observed at the genus level. Taken together, these findings indicated that the bias observed in the results about the community structure occurred primarily in OTUs with a lower abundance. The results of this study demonstrate that possible bias exists in community analyses, and researchers should therefore be conservative when drawing conclusions about community structures based on the currently available DNA extraction methods.
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Affiliation(s)
- Zhuoran Han
- Key Laboratory of Ecology and Environment Science of Higher Education Institutes, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, College of Life Science, South China Normal University, Guangzhou, China.,Tianjin Key Lab of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, China
| | - Jingfeng Sun
- Tianjin Key Lab of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, China
| | - Aijun Lv
- Tianjin Key Lab of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, China
| | - Anli Wang
- Key Laboratory of Ecology and Environment Science of Higher Education Institutes, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, College of Life Science, South China Normal University, Guangzhou, China
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Han Z, Sun J, Lv A, Sung Y, Sun X, Shi H, Hu X, Wang A, Xing K. A modified method for genomic DNA extraction from the fish intestinal microflora. AMB Express 2018; 8:52. [PMID: 29610998 PMCID: PMC5880796 DOI: 10.1186/s13568-018-0578-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 03/25/2018] [Indexed: 01/23/2023] Open
Abstract
A modified genomic DNA extraction method named the combination of lysozyme and ultrasonic lysis (CLU) method was used to analyze the fish intestinal microflora. In this method, the physical disruption and chemical lysis steps were combined, and some parameters in the key steps were adjusted. In addition, the results obtained by this method were compared with the results obtained by the Zirmil-beating cell disruption method and the QIAamp Fast DNA Stool Mini Kit. The OD260/OD280 ratio and concentration of the DNA extracted using the CLU method were 2.02 and 282.8 µg/µL, respectively; when the incubation temperatures for lysozyme and RNase were adjusted to 37 °C, those values were 2.08 and 309.8 µg/µL, respectively. On the agarose gel, a major high-intensity, discrete band of more than 10 kb was found for the CLU method. However, the smearing intensity of degraded DNA was lower when the incubation temperatures were 60 °C for lysozyme and 30 °C for RNase than when incubation temperatures of 37 °C for lysozyme and 37 °C for RNase were used. The V3 variable region of the prokaryotic 16S rDNA was amplified, and an approximately 600-bp fragment was observed when the DNA extracted using the CLU method was used as a template. The CLU method is simple and cost effective, and it yields high-quality, unsheared, high-molecular-weight DNA, which is comparable to that obtained with a commercially available kit. The extracted DNA has potential for applications in critical molecular biology techniques.
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Wang L, Dong Y, Wang S, Li L, Kong X, Lv A. First sporadic case of pathogenic Escherichia coli infection in Black swan in China. Microb Pathog 2016; 98:32-6. [PMID: 27354206 DOI: 10.1016/j.micpath.2016.06.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Revised: 06/17/2016] [Accepted: 06/24/2016] [Indexed: 10/21/2022]
Abstract
A strain of bacteria was isolated from the diseased black swan (Cygnus atratus) died from enteritis diarrhea, and designated tentatively as B-1 strain. Morphological and biochemical tests, as well as phylogenetic analysis derived from 16S rRNA and fimC gene sequencing both strongly indicated that B-1 strain is identical to Escherichia coli. Furthermore, the polymerase chain reaction single-strand conformation polymorphism (PCR-SSCP) profile of the isolate was different from that of two reference strains. Antibiotic sensitivity testing of B-1 strain was carried out by the standard Kirby-Bauer disc diffusion method. Animal experiments demonstrated that B-1 strain is pathogenic to mice and chickens. This is first sporadic case of pathogenic E. coli infection in Black swan in China.
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Affiliation(s)
- Lirong Wang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Yongjun Dong
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Sanhu Wang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Li Li
- College of Fisheries, Henan Normal University, Xinxiang, 453007, China
| | - Xianghui Kong
- College of Fisheries, Henan Normal University, Xinxiang, 453007, China
| | - Aijun Lv
- College of Fisheries, Henan Normal University, Xinxiang, 453007, China; Tianjin Key Lab. of Aqua-Ecology & Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, 300384, China.
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Chen S, Luo H, Li Y, Sun Y, Wu Q, Niu Y, Song J, Lv A, Zhu Y, Sun C, Steinmetz A, Qian Z. 454 EST analysis detects genes putatively involved in ginsenoside biosynthesis in Panax ginseng. Plant Cell Rep 2011; 30:1593-1601. [PMID: 21484331 DOI: 10.1007/s00299-011-1070-6] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Revised: 03/29/2011] [Accepted: 04/01/2011] [Indexed: 05/28/2023]
Abstract
Panax ginseng C.A. Meyer is one of the most highly valued medicinal plants in the world. To analyze the transcriptome of P. ginseng and discover the genes involved in ginsenoside biosynthesis, cDNAs derived from the total RNA of 11-year-old, wood-grown P. ginseng roots were analyzed by 454 sequencing. A total of 217,529 high quality reads (expressed sequence tags, ESTs), with an average length of 409 bases, were generated from a one-quarter run to yield 31,741 unique sequences. The majority (20,198; 63.6%) of the unique sequences were annotated using BLAST similarity searches. A total of 16,810 and 16,577 unique sequences were assigned to functional classifications and biochemical pathways based on Gene Ontology analysis and the Kyoto Encyclopedia of Genes and Genomes assignment, respectively. Nine genes involved in the biosynthesis of ginsenoside skeletons and many candidate genes putatively responsible for modification of the skeletons, including 133 cytochrome P450s and 235 glycosyltransferases, were identified. From these candidates, six transcripts encoding UDP-glycosyltransferases that were most likely to be involved in ginsenoside biosynthesis were selected. These results open a new avenue by which to explore and exploit biosynthetic and biochemical properties that may lead to drug improvement. These 454 ESTs will provide the foundation for further functional genomic research into the traditional herb P. ginseng or its closely related species.
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Affiliation(s)
- S Chen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, HaiDian, Beijing 100193, China.
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An Y, Lv A, Wu W. A colony-to-lawn method for efficient transformation of Escherichia coli. Lett Appl Microbiol 2010; 51:98-103. [PMID: 20497312 DOI: 10.1111/j.1472-765x.2010.02864.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
AIMS To develop a fast, convenient, inexpensive and efficient Escherichia coli transformation method for changing hosts of plasmids, which can also facilitate the selection of positive clones after DNA ligation and transformation. METHODS AND RESULTS A single fresh colony from plasmid-containing donor strain is picked up and suspended in 75% ethanol. Cells are pelleted and resuspended in CaCl(2) solution and lysed by repetitive freeze-thaw cycles to obtain plasmid-containing cell lysate. The E. coli recipient cells are scraped from the lawn of LB plate and directly suspended in the plasmid-containing cell lysate for transformation. Additionally, a process based on colony-to-lawn transformation and protein expression was designed and conveniently used to screen positive clones after DNA ligation and transformation. CONCLUSIONS With this method, a single colony from plasmid-containing donor strain can be directly used to transform recipient cells scraped from lawn of LB plate. Additionally, in combination with this method, screening of positive clones after DNA ligation and transformation can be convenient and time-saving. SIGNIFICANCE AND IMPACT OF THE STUDY Compared with current methods, this procedure saves the steps of plasmid extraction and competent cell preparation. Therefore, the method should be highly valuable especially for high-throughput changing hosts of plasmids during mutant library creation.
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Affiliation(s)
- Y An
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
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An Y, Ji J, Lv A, Huang R, Xiu Z. [Molecular evolution of AdoMet synthetase by DNA recombination with a novel separate-mixing method]. Mol Biol (Mosk) 2006; 40:546-53. [PMID: 16813174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
We describe a new approach to in vitro DNA recombination termed Separate-Mixing method in this study. The reaction process of this method consists of two stages: at the first stage the reaction was implemented in two parallel teams, which generated random recombination by template-switching of growing polynucleotides from primers in the presence of unidirectional single-stranded DNA fragments used as templates, and then both teams were mixed together for further extension and recombination of DNA sequences at the second stage. Because of the particular strategy, the reaction process was also accompanied by the other two processes of DNA shuffling and StEP simultaneously. Two AdoMet synthetase genes sam2 from Saccharomyces cerevisiae and metK from Escherichia coli, which have only 56% homology on the DNA level were used for recombination with Separate-Mixing method. DNA recombination was available after a single round of reaction. With sequencing of 10 randomly selected recombinants, no unshuffled parental clone was found, and also no unexpected insertion, deletion or rearrangement was detected. An evolved gene sam' was obtained after screen and selection, which could obviously increase the accumulation of AdoMet in S. cerevisiae.
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An Y, Ji J, Wu W, Lv A, Huang R, Xiu Z. Molecular evolution of adomet synthetase by DNA recombination with a novel Separate-Mixing method. Mol Biol 2006. [DOI: 10.1134/s0026893306030162] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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