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Mawardi M, Indrawati A, Wibawan IWT, Lusiastuti AM. Antimicrobial susceptibility test and antimicrobial resistance gene detection of extracellular enzyme bacteria isolated from tilapia (Oreochromis niloticus) for probiotic candidates. Vet World 2023; 16:264-271. [PMID: 37042005 PMCID: PMC10082709 DOI: 10.14202/vetworld.2023.264-271] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 01/13/2023] [Indexed: 02/13/2023] Open
Abstract
Background and Aim: Antimicrobial resistance (AMR) is a global problem that can increase mortality and morbidity rates and adversely affect health. Therefore, AMR control must be carried out in various sectors, including the fisheries sector, using probiotics. Bacteria can become resistant to antibiotics, including bacteria used for probiotics. This study aimed to isolate bacteria as potential producers of extracellular enzymes, phenotypic characterization, and antibiotic-resistant gene patterns.
Materials and Methods: In this study, 459 bacterial isolates were isolated from the stomach of tilapia in Indonesia. Tilapia was obtained from Sukabumi, Ciamis, Serang, Banjarnegara, Jayapura, Sorong, Manokwari Selatan, Takalar, Lampung, Batam, and Mandiangin. Enzymatic bacteria were identified. An antimicrobial susceptibility test was conducted by agar disk diffusion, and genotypic detection of encoding genes was performed using a molecular method.
Results: This study obtained 137 isolates (29.84%) that can produce extracellular enzymes. The highest number of E-sensitive isolates was found, including 130 isolates (94.89%). Six isolates (6/137) can produce four enzymes (amylase, protease, cellulose, and lipase), and they were sensitive to antibiotics. A total of 99 isolates can produce extracellular enzymes, and they were sensitive to antibiotics. Such isolates serve as a consortium of probiotic candidates. The isolates that are resistant to oxytetracycline (OT), erythromycin (E), tetracycline (TE), and enrofloxacin (ENR) included 15 isolates (10.95%), seven isolates (5.11%), three isolates (2.19%), and one isolate (0.73%), respectively. In addition, four isolates (2.92%) were detected as multidrug-resistant. The tet(A) gene obtained the highest result of detection of resistance genes in isolates that were intermediate and resistant to TE and OT. Isolates that serve as ENR intermediates have a high qnr(S) resistance gene.
Conclusion: The data in this study provide the latest update that bacteria can serve as a consortium of potential probiotics with antibiotic-resistant genes for the treatment of fish. Bacteria that are intermediate to antibiotics may contain resistance genes. The results of this study will improve the policy of probiotic standards in Indonesia.
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Affiliation(s)
- Mira Mawardi
- School of Veterinary Medicine and Biomedical Sciences (SVMBS), IPB University, Jl. Agatis Kampus IPB Dramaga Bogor, 16680, Indonesia; Main Center for Freshwater Aquaculture, Ministry of Marine Affairs and Fisheries, Jl. Selabintana No. 37, Selabatu, Kec, Cikole, Kota Sukabumi, Jawa Barat 43114, Indonesia
| | - Agustin Indrawati
- School of Veterinary Medicine and Biomedical Sciences (SVMBS), IPB University, Jl. Agatis Kampus IPB Dramaga Bogor, 16680, Indonesia
| | - I. Wayan Teguh Wibawan
- School of Veterinary Medicine and Biomedical Sciences (SVMBS), IPB University, Jl. Agatis Kampus IPB Dramaga Bogor, 16680, Indonesia
| | - Angela Mariana Lusiastuti
- Research Center for Veterinary Sciences, National Research and Innovation Agency, RE Martadinata 30 Bogor, Jawa Barat, Indonesia
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2
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Zhu L, Liu J, Zhou J, Wu X, Yang K, Ni Z, Liu Z, Jia H. The overlooked toxicity of environmentally persistent free radicals (EPFRs) induced by anthracene transformation to earthworms (Eisenia fetida). THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 853:158571. [PMID: 36075414 DOI: 10.1016/j.scitotenv.2022.158571] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/22/2022] [Accepted: 09/03/2022] [Indexed: 06/15/2023]
Abstract
Environmentally persistent free radicals (EPFRs) as intermediate products exist widely in the PAHs-contaminated soils, but toxicity assessment associated with EPFRs for terrestrial invertebrates remains unclear. Using the model organism Eisenia fetida, we compared the adverse effects among anthracene (ANT), anthraquinone (ANQ), and EPFRs induced by ANT transformation on clay surfaces. Our results showed that EPFRs-exposed earthworms experienced histopathological damage, which was more severe than ANT and ANQ-exposed earthworms. The source of EPFRs damage was associated with the obvious dysbiosis of reactive oxygen species in earthworms. Specifically, EPFRs trigged more severe antioxidant responses and oxidative damages (e.g., membrane lipid and DNA injury) in comparison with ANT and ANQ exposure, as evidenced by the values of integrated biomarker response (IBR) following the order of EPFRs (14.5) > ANT (12.8) > ANQ (10.9). Moreover, high-throughput sequencing found that EPFRs induced dramatic changes in the composition and structure of earthworm gut microbiota, which may involve immune and metabolism dysfunction, in turn aggravated EPFRs toxicity. Overall, the obtained information highlights the more severe injury of EPFRs to terrestrial organisms, deserving more attentions for the assessment of potential risks associated with radical intermediates in PAHs-contaminated soils.
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Affiliation(s)
- Lang Zhu
- College of Natural Resources and Environment, Northwest A & F University, Yangling 712100, China
| | - Jinbo Liu
- College of Natural Resources and Environment, Northwest A & F University, Yangling 712100, China
| | - Jinyi Zhou
- College of Natural Resources and Environment, Northwest A & F University, Yangling 712100, China
| | - Xintong Wu
- College of Natural Resources and Environment, Northwest A & F University, Yangling 712100, China
| | - Kangjie Yang
- College of Natural Resources and Environment, Northwest A & F University, Yangling 712100, China
| | - Zheng Ni
- College of Natural Resources and Environment, Northwest A & F University, Yangling 712100, China
| | - Ze Liu
- College of Natural Resources and Environment, Northwest A & F University, Yangling 712100, China
| | - Hanzhong Jia
- College of Natural Resources and Environment, Northwest A & F University, Yangling 712100, China; Key Laboratory of Low-carbon Green Agriculture in Northwestern China, Ministry of Agriculture and Rural Affairs, China.
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3
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Kalia VC, Gong C, Shanmugam R, Lee JK. Prospecting Microbial Genomes for Biomolecules and Their Applications. Indian J Microbiol 2022; 62:516-523. [PMID: 36458216 PMCID: PMC9705627 DOI: 10.1007/s12088-022-01040-x] [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: 08/02/2022] [Accepted: 09/04/2022] [Indexed: 11/26/2022] Open
Abstract
Bioactive molecules of microbial origin are finding increasing biotechnological applications. Their sources range from the terrestrial, marine, and endophytic to the human microbiome. These biomolecules have unique chemical structures and related groups, which enable them to improve the efficiency of the bioprocesses. This review focuses on the applications of biomolecules in bioremediation, agriculture, food, pharmaceutical industries, and human health.
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Affiliation(s)
- Vipin Chandra Kalia
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, 05029 Republic of Korea
| | - Chunjie Gong
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan, 430068 People’s Republic of China
| | - Ramasamy Shanmugam
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, 05029 Republic of Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, 05029 Republic of Korea
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4
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Gupta DS, Kumar MS. The implications of quorum sensing inhibition in bacterial antibiotic resistance- with a special focus on aquaculture. J Microbiol Methods 2022; 203:106602. [PMID: 36270462 DOI: 10.1016/j.mimet.2022.106602] [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: 06/12/2022] [Revised: 10/06/2022] [Accepted: 10/13/2022] [Indexed: 11/06/2022]
Abstract
The aquaculture industry is an expanding and demanding industry and due to an increase in urbanization, with rise in income of developing countries population, it offers to provide a sustainable food supply. However, the industry is facing a number of challenges, out of which few needs to be tackled immediately to maximise the productivity. An upcoming problem is the emergence of antibiotic resistant pathogens due to the unchecked use of antibiotics in aquaculture and human clinical practices. A wide variety of aquatic pathogens such as Edwardsiella, Vibrio, and Aeromonas spp. use quorum sensing (QS) systems, a regulatory process involving cell communication via signalling molecules for the collective function of pathogens which regulates the genes expression including virulent genes. Quorum sensing results in bacterial biofilms formation, which leads to their reduced susceptibility towards antimicrobial agents. The usage of quorum sensing inhibitors (QSIs) has been proposed as an attractive strategy to tackle this problem. Due to the modulation of virulence genes expression, QSIs can be used as novel and viable approach to overcome antibiotic resistance in aquaculture. In this review, we direct our attention to the quorum sensing phenomenon and its viability as a target pathway for tackling the ever-growing problem of antimicrobial resistance in aquaculture. This review also provides a concise compilation of the currently available QSIs and investigates possible natural sources for quorum quenching.
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Affiliation(s)
- Dhruv S Gupta
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM'(S) NMIMS, Vile Parle (w), Mumbai 400056, India
| | - Maushmi S Kumar
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM'(S) NMIMS, Vile Parle (w), Mumbai 400056, India.
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5
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Simón R, Docando F, Nuñez-Ortiz N, Tafalla C, Díaz-Rosales P. Mechanisms Used by Probiotics to Confer Pathogen Resistance to Teleost Fish. Front Immunol 2021; 12:653025. [PMID: 33986745 PMCID: PMC8110931 DOI: 10.3389/fimmu.2021.653025] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 03/29/2021] [Indexed: 11/13/2022] Open
Abstract
Probiotics have been defined as live microorganisms that when administered in adequate amounts confer health benefits to the host. The use of probiotics in aquaculture is an attractive bio-friendly method to decrease the impact of infectious diseases, but is still not an extended practice. Although many studies have investigated the systemic and mucosal immunological effects of probiotics, not all of them have established whether they were actually capable of increasing resistance to different types of pathogens, being this the outmost desired goal. In this sense, in the current paper, we have summarized those experiments in which probiotics were shown to provide increased resistance against bacterial, viral or parasitic pathogens. Additionally, we have reviewed what is known for fish probiotics regarding the mechanisms through which they exert positive effects on pathogen resistance, including direct actions on the pathogen, as well as positive effects on the host.
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Affiliation(s)
| | | | | | | | - Patricia Díaz-Rosales
- Fish Immunology and Pathology Laboratory, Animal Health Research Centre (CISA-INIA), Madrid, Spain
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6
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Li YX, Wang NN, Zhou YX, Lin CG, Wu JS, Chen XQ, Chen GJ, Du ZJ. Planococcus maritimus ML1206 Isolated from Wild Oysters Enhances the Survival of Caenorhabditis elegans against Vibrio anguillarum. Mar Drugs 2021; 19:md19030150. [PMID: 33809116 PMCID: PMC7999227 DOI: 10.3390/md19030150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/05/2021] [Accepted: 03/09/2021] [Indexed: 11/16/2022] Open
Abstract
With the widespread occurrence of aquaculture diseases and the broad application of antibiotics, drug-resistant pathogens have increasingly affected aquatic animals’ health. Marine probiotics, which live under high pressure in a saltwater environment, show high potential as a substitute for antibiotics in the field of aquatic disease control. In this study, twenty strains of non-hemolytic bacteria were isolated from the intestine of wild oysters and perch, and a model of Caenorhabditis elegans infected by Vibrio anguillarum was established. Based on the model, ML1206, which showed a 99% similarity of 16S rRNA sequence to Planococcus maritimus, was selected as a potential marine probiotic, with strong antibacterial capabilities and great acid and bile salt tolerance, to protect Caenorhabditis elegans from being damaged by Vibrio anguillarum. Combined with plate counting and transmission electron microscopy, it was found that strain ML1206 could significantly inhibit Vibrio anguillarum colonization in the intestinal tract of Caenorhabditis elegans. Acute oral toxicity tests in mice showed that ML1206 was safe and non-toxic. The real-time qPCR results showed a higher expression level of genes related to the antibacterial peptide (ilys-3) and detoxification (ugt-22, cyp-35A3, and cyp-14A3) in the group of Caenorhabditis elegans protected by ML1206 compared to the control group. It is speculated that ML1206, as a potential probiotic, may inhibit the infection caused by Vibrio anguillarum through stimulating Caenorhabditis elegans to secrete antibacterial effectors and detoxification proteins. This paper provides a new direction for screening marine probiotics and an experimental basis to support the potential application of ML1206 as a marine probiotic in aquaculture.
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Affiliation(s)
- Ying-Xiu Li
- Marine College, Shandong University, Weihai 264209, China; (Y.-X.L.); (N.-N.W.); (Y.-X.Z.); (C.-G.L.); (J.-S.W.); (X.-Q.C.)
| | - Nan-Nan Wang
- Marine College, Shandong University, Weihai 264209, China; (Y.-X.L.); (N.-N.W.); (Y.-X.Z.); (C.-G.L.); (J.-S.W.); (X.-Q.C.)
| | - Yan-Xia Zhou
- Marine College, Shandong University, Weihai 264209, China; (Y.-X.L.); (N.-N.W.); (Y.-X.Z.); (C.-G.L.); (J.-S.W.); (X.-Q.C.)
| | - Chun-Guo Lin
- Marine College, Shandong University, Weihai 264209, China; (Y.-X.L.); (N.-N.W.); (Y.-X.Z.); (C.-G.L.); (J.-S.W.); (X.-Q.C.)
| | - Jing-Shan Wu
- Marine College, Shandong University, Weihai 264209, China; (Y.-X.L.); (N.-N.W.); (Y.-X.Z.); (C.-G.L.); (J.-S.W.); (X.-Q.C.)
| | - Xin-Qi Chen
- Marine College, Shandong University, Weihai 264209, China; (Y.-X.L.); (N.-N.W.); (Y.-X.Z.); (C.-G.L.); (J.-S.W.); (X.-Q.C.)
| | - Guan-Jun Chen
- Marine College, Shandong University, Weihai 264209, China; (Y.-X.L.); (N.-N.W.); (Y.-X.Z.); (C.-G.L.); (J.-S.W.); (X.-Q.C.)
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China
- Correspondence: (G.J.C.); (Z.-J.D.)
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai 264209, China; (Y.-X.L.); (N.-N.W.); (Y.-X.Z.); (C.-G.L.); (J.-S.W.); (X.-Q.C.)
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China
- Correspondence: (G.J.C.); (Z.-J.D.)
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7
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Yang Y, Liu P, Li M. Tri-n-butyl phosphate induced earthworm intestinal damage by influencing nutrient absorption and energy homeostasis of intestinal epithelial cells. JOURNAL OF HAZARDOUS MATERIALS 2020; 398:122850. [PMID: 32768812 DOI: 10.1016/j.jhazmat.2020.122850] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/17/2020] [Accepted: 04/24/2020] [Indexed: 06/11/2023]
Abstract
Tri-n-butyl phosphate (TnBP) is a typical alkyl organophosphate ester that has been used for decades in various products. However, toxicity on terrestrial organisms induced by TnBP has been rarely reported though soil is a predominant sink for hydrophobic organic compounds. The objective of this study was to investigate the TnBP-induced intestinal toxicity mechanism on earthworm Eisenia fetida as well as the potential role of gut bacteria on host's health. TnBP was found to have high bioconcentrations in earthworm intestinal tract. Digestive tract degradation and digestive enzyme activities disruption associated with nutrients absorption were noticed. Using multi-omics approaches, detailed intestinal toxic mechanism of earthworms under TnBP exposure was provided. Tight junctions between small intestinal epithelial cells and osmotic equilibrium were destroyed under 10 mg/kg TnBP, leading to nutrient absorption disturbance. To satisfy the excessive energy requirements induced by TnBP, amino acids gluconeogenesis and protein degradation were detected. Moreover, TnBP significantly decreased the diversity of gut microbiota and changed their structure and function involved in hosts' health and nutrients supply. Overall, this study provides insight into the molecular mechanism of intestinal toxicity by which earthworms respond to TnBP exposure and offer important information for risk assessment of organophosphate esters on soil ecosystems.
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Affiliation(s)
- Yang Yang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China; Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Peng Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Mei Li
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China.
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8
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Wang J, Lin J, Zhang Y, Zhang J, Feng T, Li H, Wang X, Sun Q, Zhang X, Wang Y. Activity Improvement and Vital Amino Acid Identification on the Marine-Derived Quorum Quenching Enzyme MomL by Protein Engineering. Mar Drugs 2019; 17:md17050300. [PMID: 31117226 PMCID: PMC6562636 DOI: 10.3390/md17050300] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 05/17/2019] [Accepted: 05/17/2019] [Indexed: 12/25/2022] Open
Abstract
MomL is a marine-derived quorum-quenching (QQ) lactonase which can degrade various N-acyl homoserine lactones (AHLs). Intentional modification of MomL may lead to a highly efficient QQ enzyme with broad application potential. In this study, we used a rapid and efficient method combining error-prone polymerase chain reaction (epPCR), high-throughput screening and site-directed mutagenesis to identify highly active MomL mutants. In this way, we obtained two candidate mutants, MomLI144V and MomLV149A. These two mutants exhibited enhanced activities and blocked the production of pathogenic factors of Pectobacterium carotovorum subsp. carotovorum (Pcc). Besides, seven amino acids which are vital for MomL enzyme activity were identified. Substitutions of these amino acids (E238G/K205E/L254R) in MomL led to almost complete loss of its QQ activity. We then tested the effect of MomL and its mutants on Pcc-infected Chinese cabbage. The results indicated that MomL and its mutants (MomLL254R, MomLI144V, MomLV149A) significantly decreased the pathogenicity of Pcc. This study provides an efficient method for QQ enzyme modification and gives us new clues for further investigation on the catalytic mechanism of QQ lactonase.
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Affiliation(s)
- Jiayi Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Jing Lin
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Yunhui Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Jingjing Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Tao Feng
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Hui Li
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Xianghong Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Qingyang Sun
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Xiaohua Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
| | - Yan Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
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9
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Zhao J, Li X, Hou X, Quan C, Chen M. Widespread Existence of Quorum Sensing Inhibitors in Marine Bacteria: Potential Drugs to Combat Pathogens with Novel Strategies. Mar Drugs 2019; 17:md17050275. [PMID: 31072008 PMCID: PMC6562741 DOI: 10.3390/md17050275] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 04/28/2019] [Accepted: 04/29/2019] [Indexed: 12/22/2022] Open
Abstract
Quorum sensing (QS) is a phenomenon of intercellular communication discovered mainly in bacteria. A QS system consisting of QS signal molecules and regulatory protein components could control physiological behaviors and virulence gene expression of bacterial pathogens. Therefore, QS inhibition could be a novel strategy to combat pathogens and related diseases. QS inhibitors (QSIs), mainly categorized into small chemical molecules and quorum quenching enzymes, could be extracted from diverse sources in marine environment and terrestrial environment. With the focus on the exploitation of marine resources in recent years, more and more QSIs from the marine environment have been investigated. In this article, we present a comprehensive review of QSIs from marine bacteria. Firstly, screening work of marine bacteria with potential QSIs was concluded and these marine bacteria were classified. Afterwards, two categories of marine bacteria-derived QSIs were summarized from the aspects of sources, structures, QS inhibition mechanisms, environmental tolerance, effects/applications, etc. Next, structural modification of natural small molecule QSIs for future drug development was discussed. Finally, potential applications of QSIs from marine bacteria in human healthcare, aquaculture, crop cultivation, etc. were elucidated, indicating promising and extensive application perspectives of QS disruption as a novel antimicrobial strategy.
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Affiliation(s)
- Jing Zhao
- Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, Dalian 116600, China.
- College of Life Science, Dalian Minzu University, Dalian 116600, China.
| | - Xinyun Li
- Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, Dalian 116600, China.
- College of Life Science, Dalian Minzu University, Dalian 116600, China.
| | - Xiyan Hou
- Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, Dalian 116600, China.
- College of Life Science, Dalian Minzu University, Dalian 116600, China.
| | - Chunshan Quan
- Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, Dalian 116600, China.
- College of Life Science, Dalian Minzu University, Dalian 116600, China.
| | - Ming Chen
- School of Biological Engineering, Dalian Polytechnic University, Dalian 116600, China.
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10
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Torres M, Hong KW, Chong TM, Reina JC, Chan KG, Dessaux Y, Llamas I. Genomic analyses of two Alteromonas stellipolaris strains reveal traits with potential biotechnological applications. Sci Rep 2019; 9:1215. [PMID: 30718637 PMCID: PMC6361997 DOI: 10.1038/s41598-018-37720-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 11/27/2018] [Indexed: 11/08/2022] Open
Abstract
The Alteromonas stellipolaris strains PQQ-42 and PQQ-44, previously isolated from a fish hatchery, have been selected on the basis of their strong quorum quenching (QQ) activity, as well as their ability to reduce Vibrio-induced mortality on the coral Oculina patagonica. In this study, the genome sequences of both strains were determined and analyzed in order to identify the mechanism responsible for QQ activity. Both PQQ-42 and PQQ-44 were found to degrade a wide range of N-acylhomoserine lactone (AHL) QS signals, possibly due to the presence of an aac gene which encodes an AHL amidohydrolase. In addition, the different colony morphologies exhibited by the strains could be related to the differences observed in genes encoding cell wall biosynthesis and exopolysaccharide (EPS) production. The PQQ-42 strain produces more EPS (0.36 g l-1) than the PQQ-44 strain (0.15 g l-1), whose chemical compositions also differ. Remarkably, PQQ-44 EPS contains large amounts of fucose, a sugar used in high-value biotechnological applications. Furthermore, the genome of strain PQQ-42 contained a large non-ribosomal peptide synthase (NRPS) cluster with a previously unknown genetic structure. The synthesis of enzymes and other bioactive compounds were also identified, indicating that PQQ-42 and PQQ-44 could have biotechnological applications.
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Affiliation(s)
- Marta Torres
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
- Institute of Biotechnology, Biomedical Research Center (CIBM), University of Granada, Granada, Spain
- Institute for Integrative Biology of the Cell (I2BC), CEA/CNRS/University Paris-Sud, University Paris-Saclay, Gif-sur-Yvette, France
| | - Kar-Wai Hong
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Teik-Min Chong
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - José Carlos Reina
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Kok-Gan Chan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- International Genome Centre, Jiangsu University, Zhenjiang, China
| | - Yves Dessaux
- Institute for Integrative Biology of the Cell (I2BC), CEA/CNRS/University Paris-Sud, University Paris-Saclay, Gif-sur-Yvette, France.
| | - Inmaculada Llamas
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
- Institute of Biotechnology, Biomedical Research Center (CIBM), University of Granada, Granada, Spain
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11
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Kalia VC, Patel SKS, Kang YC, Lee JK. Quorum sensing inhibitors as antipathogens: biotechnological applications. Biotechnol Adv 2018; 37:68-90. [PMID: 30471318 DOI: 10.1016/j.biotechadv.2018.11.006] [Citation(s) in RCA: 167] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 10/19/2018] [Accepted: 11/18/2018] [Indexed: 12/20/2022]
Abstract
The mechanisms through which microbes communicate using signal molecules has inspired a great deal of research. Microbes use this exchange of information, known as quorum sensing (QS), to initiate and perpetuate infectious diseases in eukaryotic organisms, evading the eukaryotic defense system by multiplying and expressing their pathogenicity through QS regulation. The major issue to arise from such networks is increased bacterial resistance to antibiotics, resulting from QS-dependent mediation of the formation of biofilm, the induction of efflux pumps, and the production of antibiotics. QS inhibitors (QSIs) of diverse origins have been shown to act as potential antipathogens. In this review, we focus on the use of QSIs to counter diseases in humans as well as plants and animals of economic importance. We also discuss the challenges encountered in the potential applications of QSIs.
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Affiliation(s)
- Vipin Chandra Kalia
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea.
| | - Sanjay K S Patel
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Yun Chan Kang
- Department of Materials Science and Engineering, Korea University, Anam-Dong, Seongbuk-Gu, Seoul 02841, Republic of Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea.
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Genome-Wide Comparison Reveals a Probiotic Strain Lactococcus Lactis WFLU12 Isolated from the Gastrointestinal Tract of Olive Flounder (Paralichthys Olivaceus) Harboring Genes Supporting Probiotic Action. Mar Drugs 2018; 16:md16050140. [PMID: 29695124 PMCID: PMC5983272 DOI: 10.3390/md16050140] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 04/06/2018] [Accepted: 04/19/2018] [Indexed: 02/06/2023] Open
Abstract
Our previous study has shown that dietary supplementation with Lactococcus lactis WFLU12 can enhance the growth of olive flounder and its resistance against streptococcal infection. The objective of the present study was to use comparative genomics tools to investigate genomic characteristics of strain WFLU12 and the presence of genes supporting its probiotic action using sequenced genomes of L. lactis strains. Dispensable and singleton genes of strain WFLU12 were found to be more enriched in genes associated with metabolism (e.g., energy production and conversion, and carbohydrate transport and metabolism) than pooled dispensable and singleton genes in other L. lactis strains, reflecting WFLU12 strain-specific ecosystem origin and its ability to metabolize different energy sources. Strain WFLU12 produced antimicrobial compounds that could inhibit several bacterial fish pathogens. It possessed the nisin gene cluster (nisZBTCIPRKFEG) and genes encoding lysozyme and colicin V. However, only three other strains (CV56, IO-1, and SO) harbor a complete nisin gene cluster. We also found that L. lactis WFLU12 possessed many other important functional genes involved in stress responses to the gastrointestinal tract environment, dietary energy extraction, and metabolism to support the probiotic action of this strain found in our previous study. This strongly indicates that not all L. lactis strains can be used as probiotics. This study highlights comparative genomics approaches as very useful and powerful tools to select probiotic candidates and predict their probiotic effects.
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13
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Yang JA, Yang SH, Kim J, Kwon KK, Oh HM. Comparative genome analysis of the Flavobacteriales bacterium strain UJ101, isolated from the gut of Atergatis reticulatus. J Microbiol 2017; 55:583-591. [PMID: 28664513 DOI: 10.1007/s12275-017-7172-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 06/07/2017] [Accepted: 06/19/2017] [Indexed: 12/19/2022]
Abstract
Here we report the comparative genomic analysis of strain UJ101 with 15 strains from the family Flavobacteriaceae, using the CGExplorer program. Flavobacteriales bacterium strain UJ101 was isolated from a xanthid crab, Atergatis reticulatus, from the East Sea near Korea. The complete genome of strain UJ101 is a 3,074,209 bp, single, circular chromosome with 30.74% GC content. While the UJ101 genome contains a number of annotated genes for many metabolic pathways, such as the Embden-Meyerhof pathway, the pentose phosphate pathway, the tricarboxylic acid (TCA) cycle, and the glyoxylate cycle, genes for the Entner-Douddoroff pathway are not found in the UJ101 genome. Overall, carbon fixation processes were absent but nitrate reduction and denitrification pathways were conserved. The UJ101 genome was compared to genomes from other marine animals (three invertebrate strains and 5 fish strains) and other marine animal- derived genera. Notable results by genome comparisons showed that UJ101 is capable of denitrification and nitrate reduction, and that biotin-thiamine pathway participation varies among marine bacteria; fish-dwelling bacteria, freeliving bacteria, invertebrate-dwelling bacteria, and strain UJ101. Pan-genome analysis of the 16 strains in this study included 7,220 non-redundant genes that covered 62% of the pan-genome. A core-genome of 994 genes was present and consisted of 8% of the genes from the pan-genome. Strain UJ101 is a symbiotic hetero-organotroph isolated from xanthid crab, and is a metabolic generalist with nitrate-reducing abilities but without the ability to synthesize biotin. There is a general tendency of UJ101 and some fish pathogens to prefer thiamine-dependent glycolysis to gluconeogenesis. Biotin and thiamine auxotrophy or prototrophy may be used as important markers in microbial community studies.
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Affiliation(s)
- Jhung-Ahn Yang
- Departments of Marine-Bio Convergence Science, Specialized Graduate School Science & Technology Convergence, Pukyong National University, Busan, 48547, Republic of Korea
| | - Sung-Hyun Yang
- Marine Biotechnology Research Division, Korea Institute of Ocean Science & Technology, Ansan, 15627, Republic of Korea
| | - Junghee Kim
- Departments of Marine-Bio Convergence Science, Specialized Graduate School Science & Technology Convergence, Pukyong National University, Busan, 48547, Republic of Korea
| | - Kae Kyoung Kwon
- Marine Biotechnology Research Division, Korea Institute of Ocean Science & Technology, Ansan, 15627, Republic of Korea
| | - Hyun-Myung Oh
- Departments of Marine-Bio Convergence Science, Specialized Graduate School Science & Technology Convergence, Pukyong National University, Busan, 48547, Republic of Korea.
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14
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A novel stress response mechanism, triggered by indole, involved in quorum quenching enzyme MomL and iron-sulfur cluster in Muricauda olearia Th120. Sci Rep 2017; 7:4252. [PMID: 28652609 PMCID: PMC5484670 DOI: 10.1038/s41598-017-04606-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 06/07/2017] [Indexed: 11/28/2022] Open
Abstract
Indole, as a signal molecule, is involved in multiple physiological behavior including biofilm formation, antibiotic resistance and virulence. In this study, we demonstrated that indole was involved in iron deficient and H2O2 stress response in Muricauda olearia Th120. Transcriptome analysis showed that totally 206 genes were regulated by exogenous indole. Besides, momL-suf gene cluster, consisting of quorum quenching enzyme coding gene momL and iron-sulfur biosynthetic genes suf, were involved in indole-induced stress response pathway. The result indicated that indole not only up-regulated momL-suf gene cluster, but also enhanced the MomL secretion and the growth rates of MomL-bearing strains in H2O2 stress and iron deficient culture conditions. Co-incubation of M. olearia Th120 and Pectobacterium carotovorum subsp. carotovorum under H2O2 condition revealed that M. olearia Th120 bearing MomL possessed an increased competitive advantage, whereas its competitor had a reduced survival. The phenomenon that quorum quenching enzyme is triggered by stress factor has been rarely reported. The study also opens a new clue to explore the indole function towards quorum quenching factor in bacteria.
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15
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Mayer C, Romero M, Muras A, Otero A. Aii20J, a wide-spectrum thermostable N-acylhomoserine lactonase from the marine bacterium Tenacibaculum sp. 20J, can quench AHL-mediated acid resistance in Escherichia coli. Appl Microbiol Biotechnol 2015; 99:9523-39. [PMID: 26092757 DOI: 10.1007/s00253-015-6741-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 05/24/2015] [Accepted: 05/29/2015] [Indexed: 11/25/2022]
Abstract
Acyl homoserine lactones (AHLs) are produced by many Gram-negative bacteria to coordinate gene expression in cellular density dependent mechanisms known as quorum sensing (QS). Since the disruption of the communication systems significantly reduces virulence, the inhibition of quorumsensing processes or quorum quenching (QQ) represents an interesting anti-pathogenic strategy to control bacterial infections. Escherichia coli does not produce AHLs but possesses an orphan AHL receptor, SdiA, which is thought to be able to sense the QS signals produced by other bacteria and controls important traits as the expression of glutamate-dependent acid resistance mechanism, therefore constituting a putative target for QQ. A novel AHL-lactonase, named Aii20J, has been identified, cloned and over expressed from the marine bacterium Tenacibaculum sp. strain 20 J presenting a wide-spectrum QQ activity. The enzyme, belonging to the metallo-β-lactamase family, shares less than 31 % identity with the lactonase AiiA from Bacillus spp. Aii20J presents a much higher specific activity than the Bacillus enzyme, maintains its activity after incubation at 100 ºC for 10 minutes, is resistant to protease K and α-chymotrypsin, and is unaffected by wide ranges of pH. The addition of Aii20J (20 μg/mL) to cultures of E. coli K-12 to which OC6-HSL was added resulted in a significant reduction in cell viability in comparison with the acidresistant cultures derived from the presence of the signal. Results confirm the interaction between AHLs and SdiA in E. coli for the expression of virulence-related genes and reveal the potential use of Aii20J as anti-virulence strategy against important bacterial pathogens and in other biotechnological applications.
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Affiliation(s)
- C Mayer
- Department of Microbiology and Parasitology, Faculty of Biology-CIBUS, University of Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - M Romero
- Department of Microbiology and Parasitology, Faculty of Biology-CIBUS, University of Santiago de Compostela, 15782, Santiago de Compostela, Spain
- School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - A Muras
- Department of Microbiology and Parasitology, Faculty of Biology-CIBUS, University of Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - A Otero
- Department of Microbiology and Parasitology, Faculty of Biology-CIBUS, University of Santiago de Compostela, 15782, Santiago de Compostela, Spain.
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