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Geng T, Luo L, Ruan X, Shen B, Fang R, Zhao J, Zhou Y. Drug resistance and genetic characteristics of one Eimeria tenella isolate from Xiantao, Hubei Province, China. Parasitol Res 2024; 123:289. [PMID: 39096422 DOI: 10.1007/s00436-024-08310-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 07/26/2024] [Indexed: 08/05/2024]
Abstract
Chicken coccidiosis causes retarded growth and low production performance in poultry, resulting in huge economic losses to the poultry industry. In order to prevent and control chicken coccidiosis, great efforts have been made to develop new drugs and vaccines, which require pure isolates of Eimeria spp. In this study, we obtained the Eimeira tenella Xiantao isolate by single oocyst isolation technology and compared its genome with the reference genome GCF_000499545.2_ETH001 of the Houghton strain. The results of the comparative genomic analysis indicated that the genome of this isolate contained 46,888 single nucleotide polymorphisms (SNPs). There were 15,107 small insertion and deletion variations (indels), 1693 structural variations (SV), and 3578 copy number variations (CNV). In addition, 64 broilers were used to determine the resistance profile of Xiantao strain. Drug susceptibility testing revealed that this isolate was completely resistant to monensin, diclazuril, halofuginone, sulfachlorpyrazine sodium, and toltrazuril, but sensitive to decoquinate. These data improve our understanding of drug resistance in avian coccidia.
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Affiliation(s)
- Tiantian Geng
- Key Laboratory Preventive Veterinary of Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Liyan Luo
- Key Laboratory Preventive Veterinary of Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Xiaodie Ruan
- Key Laboratory Preventive Veterinary of Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Bang Shen
- Key Laboratory Preventive Veterinary of Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Shizishan St. 1, Wuhan, 430070, Hubei, PR China
| | - Rui Fang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Shizishan St. 1, Wuhan, 430070, Hubei, PR China
| | - Junlong Zhao
- Key Laboratory Preventive Veterinary of Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Shizishan St. 1, Wuhan, 430070, Hubei, PR China
- Shanchuan Biotechnology (Wuhan) Co., Ltd, Wuhan, PR China
| | - Yanqin Zhou
- Key Laboratory Preventive Veterinary of Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China.
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Shizishan St. 1, Wuhan, 430070, Hubei, PR China.
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Lee Y, Hwang S, Kim W, Kim JH, Palsson BO, Cho BK. CRISPR-aided genome engineering for secondary metabolite biosynthesis in Streptomyces. J Ind Microbiol Biotechnol 2024; 51:kuae009. [PMID: 38439699 PMCID: PMC10949845 DOI: 10.1093/jimb/kuae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 03/02/2024] [Indexed: 03/06/2024]
Abstract
The demand for discovering novel microbial secondary metabolites is growing to address the limitations in bioactivities such as antibacterial, antifungal, anticancer, anthelmintic, and immunosuppressive functions. Among microbes, the genus Streptomyces holds particular significance for secondary metabolite discovery. Each Streptomyces species typically encodes approximately 30 secondary metabolite biosynthetic gene clusters (smBGCs) within its genome, which are mostly uncharacterized in terms of their products and bioactivities. The development of next-generation sequencing has enabled the identification of a large number of potent smBGCs for novel secondary metabolites that are imbalanced in number compared with discovered secondary metabolites. The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) system has revolutionized the translation of enormous genomic potential into the discovery of secondary metabolites as the most efficient genetic engineering tool for Streptomyces. In this review, the current status of CRISPR/Cas applications in Streptomyces is summarized, with particular focus on the identification of secondary metabolite biosynthesis gene clusters and their potential applications.This review summarizes the broad range of CRISPR/Cas applications in Streptomyces for natural product discovery and production. ONE-SENTENCE SUMMARY This review summarizes the broad range of CRISPR/Cas applications in Streptomyces for natural product discovery and production.
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Affiliation(s)
- Yongjae Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Soonkyu Hwang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Woori Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Ji Hun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Bernhard O Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby 2800, Denmark
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
- Graduate school of Engineering Biology, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
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Nikolaidis M, Hesketh A, Frangou N, Mossialos D, Van de Peer Y, Oliver SG, Amoutzias GD. A panoramic view of the genomic landscape of the genus Streptomyces. Microb Genom 2023; 9:mgen001028. [PMID: 37266990 PMCID: PMC10327506 DOI: 10.1099/mgen.0.001028] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/05/2023] [Indexed: 06/03/2023] Open
Abstract
We delineate the evolutionary plasticity of the ecologically and biotechnologically important genus Streptomyces, by analysing the genomes of 213 species. Streptomycetes genomes demonstrate high levels of internal homology, whereas the genome of their last common ancestor was already complex. Importantly, we identify the species-specific fingerprint proteins that characterize each species. Even among closely related species, we observed high interspecies variability of chromosomal protein-coding genes, species-level core genes, accessory genes and fingerprints. Notably, secondary metabolite biosynthetic gene clusters (smBGCs), carbohydrate-active enzymes (CAZymes) and protein-coding genes bearing the rare TTA codon demonstrate high intraspecies and interspecies variability, which emphasizes the need for strain-specific genomic mining. Highly conserved genes, such as those specifying genus-level core proteins, tend to occur in the central region of the chromosome, whereas those encoding proteins with evolutionarily volatile species-level fingerprints, smBGCs, CAZymes and TTA-codon-bearing genes are often found towards the ends of the linear chromosome. Thus, the chromosomal arms emerge as the part of the genome that is mainly responsible for rapid adaptation at the species and strain level. Finally, we observed a moderate, but statistically significant, correlation between the total number of CAZymes and three categories of smBGCs (siderophores, e-Polylysin and type III lanthipeptides) that are related to competition among bacteria.
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Affiliation(s)
- Marios Nikolaidis
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece
| | - Andrew Hesketh
- School of Applied Sciences, University of Brighton, Huxley Building, Lewes Road, Brighton BN2 4GJ, UK
| | - Nikoletta Frangou
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece
| | - Dimitris Mossialos
- Microbial Biotechnology-Molecular Bacteriology-Virology Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9054 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9054 Ghent, Belgium
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Stephen G. Oliver
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Grigorios D. Amoutzias
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece
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