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Le LA, Nguyen-Hoang TP, Huynh VP, Nguyen TH, Nguyen TV, Ho-Huynh TD. Microbiome dataset analysis from a shrimp pond in Ninh Thuan, Vietnam using shotgun metagenomics. Data Brief 2020; 31:105731. [PMID: 32509936 PMCID: PMC7264489 DOI: 10.1016/j.dib.2020.105731] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 05/13/2020] [Indexed: 11/25/2022] Open
Abstract
Vietnam is one of the top shrimp producing and exporting countries in the world [1]. However, viral and bacterial epidemic diseases cause severe damages to shrimp farming, resulting in millions of US dollars losses annually [2]. Furthermore, inappropriate use of antibiotics in shrimp rearing lead to increased emergence of drug resistant pathogens [3]. Current practices for water quality control, mostly based on chemical and physical parameters; neglected biological criteria necessary for maintaining pond health. Ninh Thuan is a region situated in the South Central Coast of Vietnam. Due to its geographic location, a large part of this region is dedicated to shrimp (Litopenaeus vannamei) post-larvae production and rearing. This article presents a microbiome dataset from two water samples collected in a shrimp rearing pond in Ninh Thuan. We used Oxford Nanopore Technologies (ONT) for metagenomic sequencing of the samples to characterize microbial communities and antibiotic resistance profiles. The metagenome dataset generated will provide an understanding and comparison framework of the microbial diversity and functionality among shrimp ponds with potential application in health management and shrimp rearing industry.
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Affiliation(s)
- Lan-Anh Le
- Khoa Thuong Biotechnology Company Limited, No 17, Street 4, Phong Phu, Binh Chanh, Ho Chi Minh, Vietnam
| | - Thien-Phuc Nguyen-Hoang
- Department of Genetics, Faculty of Biology and Biotechnology, University of Science, VNU-HCM, 227 Nguyen Van Cu Street, Ward 4, District 5, Ho Chi Minh, Vietnam
| | - Van-Phuc Huynh
- Khoa Thuong Biotechnology Company Limited, No 17, Street 4, Phong Phu, Binh Chanh, Ho Chi Minh, Vietnam
| | - Tan-Huy Nguyen
- Khoa Thuong Biotechnology Company Limited, No 17, Street 4, Phong Phu, Binh Chanh, Ho Chi Minh, Vietnam
| | - Thuy-Vy Nguyen
- Department of Genetics, Faculty of Biology and Biotechnology, University of Science, VNU-HCM, 227 Nguyen Van Cu Street, Ward 4, District 5, Ho Chi Minh, Vietnam
| | - Thuy-Duong Ho-Huynh
- Khoa Thuong Biotechnology Company Limited, No 17, Street 4, Phong Phu, Binh Chanh, Ho Chi Minh, Vietnam
- Department of Genetics, Faculty of Biology and Biotechnology, University of Science, VNU-HCM, 227 Nguyen Van Cu Street, Ward 4, District 5, Ho Chi Minh, Vietnam
- Research Center for Genetics and Reproductive Health, School of Medicine, VNU-HCM, 6 Residential area, Linh Trung, Thu Duc, Ho Chi Minh, Vietnam
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Peng Z, Hu Z, Li Z, Li X, Jia C, Zhang X, Wu B, Chen H, Wang X. Characteristics of a Colistin-Resistant Escherichia coli ST695 Harboring the Chromosomally-Encoded m cr-1 Gene. Microorganisms 2019; 7:microorganisms7110558. [PMID: 31726755 PMCID: PMC6920969 DOI: 10.3390/microorganisms7110558] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 10/23/2019] [Revised: 11/08/2019] [Accepted: 11/09/2019] [Indexed: 11/23/2022] Open
Abstract
Enterobacteriaceae having chromosomally-encoded mcr-1 is rarely reported. In this study, we recovered a chromosomal mcr-1 carrying Escherichia coli, designated HeN100, from the feces of a diarrheal pig in China. Antimicrobial susceptibility testing showed that HeN100 was resistant to three aminoglycosides, twelve β-lactams including three carbapenems, one phenicol, two tetracyclines, two fluoroquinolones, nitrofurantoin, and colistin tested. Oxford Nanopore MinION sequencing revealed that the complete genomes of the multidrug resistant (MDR) HeN100 consisted of a single circular chromosome and five circular plasmids. Bioinformatical analysis determined HeN100 as ST695 and it contained many acquired resistance genes responsible for its MDR phenotypes, including colistin resistance mcr-1 and the carbapenem resistance blaNDM-1, and most of these genes were located on plasmids. However, the mcr-1 was found on the chromosome, and it was located between an IS30-like element ISApl1 and a PAP2-like encoding gene. These three genes consisted of an “ISApl1-mcr-1-orf” segment and inserted in high AT-rich regions. Finally, we found the blaNDM-1 was carried on an IncFII type conjugative plasmid. The conjugation frequency of this plasmid was 7.61 ± 2.11 × 10−5 per recipient, and its conjugation conferred resistance to carbapenems and other β-lactams, as well as aminoglycosides. The spread of this mcr-1/blaNDM-1-carrying E. coli ST695 represents a great concern of public health.
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Affiliation(s)
- Zhong Peng
- State Key Laboratory of Agricultural Microbiology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Z.P.); (Z.H.); (Z.L.); (X.L.); (C.J.); (X.Z.); (B.W.); (H.C.)
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, China
| | - Zizhe Hu
- State Key Laboratory of Agricultural Microbiology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Z.P.); (Z.H.); (Z.L.); (X.L.); (C.J.); (X.Z.); (B.W.); (H.C.)
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, China
| | - Zugang Li
- State Key Laboratory of Agricultural Microbiology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Z.P.); (Z.H.); (Z.L.); (X.L.); (C.J.); (X.Z.); (B.W.); (H.C.)
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaosong Li
- State Key Laboratory of Agricultural Microbiology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Z.P.); (Z.H.); (Z.L.); (X.L.); (C.J.); (X.Z.); (B.W.); (H.C.)
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, China
| | - Chaoying Jia
- State Key Laboratory of Agricultural Microbiology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Z.P.); (Z.H.); (Z.L.); (X.L.); (C.J.); (X.Z.); (B.W.); (H.C.)
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaoxue Zhang
- State Key Laboratory of Agricultural Microbiology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Z.P.); (Z.H.); (Z.L.); (X.L.); (C.J.); (X.Z.); (B.W.); (H.C.)
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, China
| | - Bin Wu
- State Key Laboratory of Agricultural Microbiology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Z.P.); (Z.H.); (Z.L.); (X.L.); (C.J.); (X.Z.); (B.W.); (H.C.)
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Z.P.); (Z.H.); (Z.L.); (X.L.); (C.J.); (X.Z.); (B.W.); (H.C.)
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiangru Wang
- State Key Laboratory of Agricultural Microbiology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Z.P.); (Z.H.); (Z.L.); (X.L.); (C.J.); (X.Z.); (B.W.); (H.C.)
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence: ; Tel.: +86-27-87287290
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McLeod A, Fagerlund A, Rud I, Axelsson L. Large Plasmid Complement Resolved: Complete Genome Sequencing of Lactobacillus plantarum MF1298, a Candidate Probiotic Strain Associated with Unfavorable Effect. Microorganisms 2019; 7:E262. [PMID: 31416278 DOI: 10.3390/microorganisms7080262] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 06/21/2019] [Revised: 08/08/2019] [Accepted: 08/14/2019] [Indexed: 12/27/2022] Open
Abstract
Considerable attention has been given to the species Lactobacillus plantarum regarding its probiotic potential. L. plantarum strains have shown health benefits in several studies, and even nonstrain-specific claims are allowed in certain markets. L. plantarum strain MF1298 was considered a candidate probiotic, demonstrating in vitro probiotic properties and the ability to survive passage through the human intestinal tract. However, the strain showed an unfavorable effect on symptoms in subjects with irritable bowel syndrome in a clinical trial. The properties and the genome of this strain are thus of general interest. Obtaining the complete genome of strain MF1298 proved difficult due to its large plasmid complement. Here, we exploit a combination of sequencing approaches to obtain the complete chromosome and plasmid assemblies of MF1298. The Oxford Nanopore Technologies MinION long-read sequencer was particularly useful in resolving the unusually large number of plasmids in the strain, 14 in total. The complete genome sequence of 3,576,440 basepairs contains 3272 protein-encoding genes, of which 315 are located on plasmids. Few unique regions were found in comparison with other L. plantarum genomes. Notably, however, one of the plasmids contains genes related to vitamin B12 (cobalamin) turnover and genes encoding bacterial reverse transcriptases, features not previously reported for L. plantarum. The extensive plasmid information will be important for future studies with this strain.
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