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Kim YS, Hwang EM, Jeong CM, Cha CJ. Flavobacterium psychrotrophum sp. nov. and Flavobacterium panacagri sp. nov., Isolated from Freshwater and Soil. J Microbiol 2023; 61:891-901. [PMID: 37851309 DOI: 10.1007/s12275-023-00081-1] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 10/19/2023]
Abstract
Two novel bacterial strains CJ74T and CJ75T belonging to the genus Flavobacterium were isolated from freshwater of Han River and ginseng soil, South Korea, respectively. Strain CJ74T was Gram-stain-negative, aerobic, rod-shaped, non-motile, and non-flagellated, and did not produce flexirubin-type pigments. Strain CJ75T was Gram-stain-negative, aerobic, rod-shaped, motile by gliding, and non-flagellated, and produced flexirubin-type pigments. Both strains were shown to grow optimally at 30 °C in the absence of NaCl on R2A medium. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains CJ74T and CJ75T belonged to the genus Flavobacterium and were most closely related to Flavobacterium niveum TAPW14T and Flavobacterium foetidum CJ42T with 96.17% and 97.29% 16S rRNA sequence similarities, respectively. Genomic analyses including the reconstruction of phylogenomic tree, average nucleotide identity, and digital DNA-DNA hybridization suggested that they were novel species of the genus Flavobacterium. Both strains contained menaquinone 6 (MK-6) as the primary respiratory quinone and phosphatidylethanolamine as a major polar lipid. The predominant fatty acids of both strains were iso-C15:0 and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c). Based on the polyphasic taxonomic study, strains CJ74T and CJ75T represent novel species of the genus Flavobacterium, for which names Flavobacterium psychrotrophum sp. nov. and Flavobacterium panacagri sp. nov. are proposed, respectively. The type strains are CJ74T (=KACC 19819T =JCM 32889T) and CJ75T (=KACC 23149T =JCM 36132T).
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Affiliation(s)
- Yong-Seok Kim
- Department or Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Eun-Mi Hwang
- Department or Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Chang-Myeong Jeong
- Department or Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Chang-Jun Cha
- Department or Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea.
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2
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Yin X, Chen X, Jiang XT, Yang Y, Li B, Shum MHH, Lam TTY, Leung GM, Rose J, Sanchez-Cid C, Vogel TM, Walsh F, Berendonk TU, Midega J, Uchea C, Frigon D, Wright GD, Bezuidenhout C, Picão RC, Ahammad SZ, Nielsen PH, Hugenholtz P, Ashbolt NJ, Corno G, Fatta-Kassinos D, Bürgmann H, Schmitt H, Cha CJ, Pruden A, Smalla K, Cytryn E, Zhang Y, Yang M, Zhu YG, Dechesne A, Smets BF, Graham DW, Gillings MR, Gaze WH, Manaia CM, van Loosdrecht MCM, Alvarez PJJ, Blaser MJ, Tiedje JM, Topp E, Zhang T. Toward a Universal Unit for Quantification of Antibiotic Resistance Genes in Environmental Samples. Environ Sci Technol 2023. [PMID: 37310875 DOI: 10.1021/acs.est.3c00159] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Surveillance of antibiotic resistance genes (ARGs) has been increasingly conducted in environmental sectors to complement the surveys in human and animal sectors under the "One-Health" framework. However, there are substantial challenges in comparing and synthesizing the results of multiple studies that employ different test methods and approaches in bioinformatic analysis. In this article, we consider the commonly used quantification units (ARG copy per cell, ARG copy per genome, ARG density, ARG copy per 16S rRNA gene, RPKM, coverage, PPM, etc.) for profiling ARGs and suggest a universal unit (ARG copy per cell) for reporting such biological measurements of samples and improving the comparability of different surveillance efforts.
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Affiliation(s)
- Xiaole Yin
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam, 99077 Hong Kong, China
| | - Xi Chen
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam, 99077 Hong Kong, China
| | - Xiao-Tao Jiang
- Microbiome Research Centre, St George and Sutherland Clinical School, University of New South Wales, 2052 Sydney, Australia
| | - Ying Yang
- School of Marine Sciences, Sun Yat-sen University, 519082 Zhuhai, China
| | - Bing Li
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, F518055 Shenzhen, China
| | - Marcus Ho-Hin Shum
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Pokfulam, 999077 Hong Kong, China
| | - Tommy T Y Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Pokfulam, 999077 Hong Kong, China
| | - Gabriel M Leung
- Laboratory of Data Discovery for Health, Hong Kong Science & Technology Parks, New Territories, 99077 Hong Kong, China
| | - Joan Rose
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, 48824 Michigan, United States
| | - Concepcion Sanchez-Cid
- Environmental Microbial Genomics, CNRS UMR 5005 Laboratoire Ampère, École Centrale de Lyon, Université Claude Bernard Lyon1, Université de Lyon, 69130 Écully, France
| | - Timothy M Vogel
- Environmental Microbial Genomics, CNRS UMR 5005 Laboratoire Ampère, École Centrale de Lyon, Université Claude Bernard Lyon1, Université de Lyon, 69130 Écully, France
| | - Fiona Walsh
- Department of Biology, Maynooth University, Maynooth, R51 Co. Kildare, Ireland
| | - Thomas U Berendonk
- Faculty of Environmental Sciences, Technische Universität Dresden, Institute for Hydrobiology, 01217 Dresden, Germany
| | | | | | - Dominic Frigon
- Department of Civil Engineering and Applied Mechanics, McGill University, 817 Sherbrooke St. West, Montreal, H3A 0C3 Quebec, Canada
| | - Gerard D Wright
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, L8N 3Z5 Ontario, Canada
| | - Carlos Bezuidenhout
- Unit for Environmental Sciences and Management (UESM)-Microbiology, North-West University, 2531 Potchefstroom, South Africa
| | - Renata C Picão
- Medical Microbiology Department, Paulo de Góes Microbiology Institute of the Federal University of Rio de Janeiro, 21941-902 Rio de Janeiro, Brazil
| | - Shaikh Z Ahammad
- Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, 110016 New Delhi, India
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, 9210 Aalborg, Denmark
| | - Philip Hugenholtz
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, 4072 Queensland, Australia
| | - Nicholas J Ashbolt
- Faculty of Science and Engineering, Southern Cross University, Bilinga, 4225 Queensland, Australia
| | - Gianluca Corno
- Molecular Ecology Group (MEG), Water Research Institute, National Research Council of Italy (CNR-IRSA), 28922 Verbania, Italy
| | - Despo Fatta-Kassinos
- Department of Civil and Environmental Engineering and Nireas International Water Research Center, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | - Helmut Bürgmann
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
| | - Heike Schmitt
- Centre for Zoonoses and Environmental Microbiology-Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721 Bilthoven, The Netherlands
- Department of Biotechnology, Delft University of Technology, 2628 Delft, the Netherlands
| | - Chang-Jun Cha
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, 17546 Anseong, Republic of Korea
| | - Amy Pruden
- The Charles Edward Via, Jr., Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, 24060 Virginia, United States
| | - Kornelia Smalla
- Julius Kühn Institute (JKI) Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, 38104 Braunschweig, Germany
| | - Eddie Cytryn
- Department of Soil Chemistry, Plant Nutrition and Microbiology, Institute of Soil, Water and Environmental Sciences, The Volcani Institute, Agricultural Research Organization, 7528809 Rishon LeZion, Israel
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085 Beijing, China
| | - Min Yang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085 Beijing, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 361021 Xiamen, China
| | - Arnaud Dechesne
- Department of Environmental and Resource Engineering, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Barth F Smets
- Department of Environmental and Resource Engineering, Technical University of Denmark, 2800 Lyngby, Denmark
| | - David W Graham
- School of Engineering, Newcastle University, NE1 7RU Newcastle Upon Tyne, U.K
| | - Michael R Gillings
- School of Natural Sciences and ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, 2109 New South Wales, Australia
| | - William H Gaze
- University of Exeter Medical School, Environment and Sustainability Institute, University of Exeter, TR10 9FE Cornwall, U.K
| | - Célia M Manaia
- Universidade Católica Portuguesa, CBQF-Centro de Biotecnologia e Química Fina-Laboratório Associado, Escola Superior de Biotecnologia, 4169-005 Porto, Portugal
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Pedro J J Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, 77005 Texas, United States
| | - Martin J Blaser
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, 08854 New Jersey, United States
| | - James M Tiedje
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, 48824 Michigan, United States
| | - Edward Topp
- London Research and Development Centre (LRDC), Agriculture and Agri-Food Canada, London, N5V 4T3 Ontario, Canada
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam, 99077 Hong Kong, China
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Kim JJ, Seong HJ, Johnson TA, Cha CJ, Sul WJ, Chae JC. Persistence of antibiotic resistance from animal agricultural effluents to surface water revealed by genome-centric metagenomics. J Hazard Mater 2023; 457:131761. [PMID: 37290355 DOI: 10.1016/j.jhazmat.2023.131761] [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] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 05/25/2023] [Accepted: 06/01/2023] [Indexed: 06/10/2023]
Abstract
Concerns about antibiotic resistance genes (ARGs) released from wastewaters of livestock or fish farming into the natural environment are increasing, but studies on unculturable bacteria related to the dissemination of antibiotic resistance are limited. Here, we reconstructed 1100 metagenome-assembled genomes (MAGs) to assess the impact of microbial antibiotic resistome and mobilome in wastewaters discharged to Korean rivers. Our results indicate that ARGs harbored in the MAGs were disseminated from wastewater effluents into downstream rivers. Moreover, it was found that ARGs are more commonly co-localized with mobile genetic elements (MGEs) in agricultural wastewater than in river water. Among the effluent-derived phyla, uncultured members of the superphylum Patescibacteria possessed a high number of MGEs, along with co-localized ARGs. Our findings suggest that members of the Patesibacteria are a potential vector for propagating ARGs into the environmental community. Therefore, we propose that the dissemination of ARGs by uncultured bacteria should be further investigated in multiple environments.
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Affiliation(s)
- Jin Ju Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Hoon Je Seong
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea; Korean Medicine Data Division, Korea Institute of Oriental Medicine, Daejeon 34054, Republic of Korea
| | - Timothy A Johnson
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, United States
| | - Chang-Jun Cha
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Woo Jun Sul
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea.
| | - Jong-Chan Chae
- Division of Biotechnology, Jeonbuk National University, Iksan 54596, Republic of Korea.
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Lee K, Raguideau S, Sirén K, Asnicar F, Cumbo F, Hildebrand F, Segata N, Cha CJ, Quince C. Population-level impacts of antibiotic usage on the human gut microbiome. Nat Commun 2023; 14:1191. [PMID: 36864029 PMCID: PMC9981903 DOI: 10.1038/s41467-023-36633-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 02/06/2023] [Indexed: 03/04/2023] Open
Abstract
The widespread usage of antimicrobials has driven the evolution of resistance in pathogenic microbes, both increased prevalence of antimicrobial resistance genes (ARGs) and their spread across species by horizontal gene transfer (HGT). However, the impact on the wider community of commensal microbes associated with the human body, the microbiome, is less well understood. Small-scale studies have determined the transient impacts of antibiotic consumption but we conduct an extensive survey of ARGs in 8972 metagenomes to determine the population-level impacts. Focusing on 3096 gut microbiomes from healthy individuals not taking antibiotics we demonstrate highly significant correlations between both the total ARG abundance and diversity and per capita antibiotic usage rates across ten countries spanning three continents. Samples from China were notable outliers. We use a collection of 154,723 human-associated metagenome assembled genomes (MAGs) to link these ARGs to taxa and detect HGT. This reveals that the correlations in ARG abundance are driven by multi-species mobile ARGs shared between pathogens and commensals, within a highly connected central component of the network of MAGs and ARGs. We also observe that individual human gut ARG profiles cluster into two types or resistotypes. The less frequent resistotype has higher overall ARG abundance, is associated with certain classes of resistance, and is linked to species-specific genes in the Proteobacteria on the periphery of the ARG network.
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Affiliation(s)
- Kihyun Lee
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
- CJ Bioscience, Seoul, 04527, Republic of Korea
| | | | - Kimmo Sirén
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Francesco Asnicar
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Fabio Cumbo
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Falk Hildebrand
- Organisms and Ecosystems, Earlham Institute, Norwich, NR4 7UZ, UK
- Gut Microbes and Health, Quadram Institute, Norwich, NR4 7UQ, UK
| | - Nicola Segata
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Chang-Jun Cha
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea.
| | - Christopher Quince
- Organisms and Ecosystems, Earlham Institute, Norwich, NR4 7UZ, UK.
- Gut Microbes and Health, Quadram Institute, Norwich, NR4 7UQ, UK.
- Warwick Medical School, University of Warwick, Coventry, CV4 7HL, UK.
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Kim M, Kim YS, Cha CJ. Chryseobacterium paludis sp. nov. and Chryseobacterium foetidum sp. nov. Isolated from the Aquatic Environment, South Korea. J Microbiol 2023; 61:37-47. [PMID: 36723793 DOI: 10.1007/s12275-022-00008-2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 02/02/2023]
Abstract
Two novel bacterial species CJ51T and CJ63T belonging to the genus Chryseobacterium were isolated from the Upo wetland and the Han River, South Korea, respectively. Cells of these strains were Gram-stain-negative, aerobic, non-motile, rod-shaped, and catalase- and oxidase-positive. Both strains were shown to grow optimally at 30 °C and pH 7 in the absence of NaCl on tryptic soy agar. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains CJ51T and CJ63T belonged to the genus Chryseobacterium and were most closely related to Chryseobacterium piperi CTMT and Chryseobacterium piscicola VQ-6316sT with 98.47% and 98.46% 16S rRNA sequence similarities, respectively. The average nucleotide identity values of strains CJ51T and CJ63T with its closely related type strains Chryseobacterium piperi CTMT and Chryseobacterium piscicola VQ-6316sT were 81.9% and 82.1%, respectively. The major fatty acids of strains CJ51T and CJ63T were iso-C15:0, iso-C17:0 3-OH and summed feature 9 (C16:0 10-methyl and/or iso-C17:1ω9c). Menaquinone 6 (MK-6) was identified as the primary respiratory quinone in both strains. The major polar lipids of strains CJ51T and CJ63T were phosphatidylethanolamine and several unidentified amino lipids and lipids. Based on polyphasic taxonomy data, strains CJ51T and CJ63T represent novel species of the genus Chryseobacterium, for which names Chryseobacterium paludis sp. nov. and Chryseobacterium foetidum sp. nov. are proposed respectively. The type strains are CJ51T (= KACC 22749T = JCM 35632T) and CJ63T (= KACC 22750T = JCM 35633T).
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Affiliation(s)
- Miryung Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Yong-Seok Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Chang-Jun Cha
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea.
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Kim DW, Ahn JH, Cha CJ. Biodegradation of plastics: mining of plastic-degrading microorganisms and enzymes using metagenomics approaches. J Microbiol 2022; 60:969-976. [DOI: 10.1007/s12275-022-2313-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/15/2022] [Accepted: 09/15/2022] [Indexed: 11/29/2022]
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Lee DH, Cha JH, Kim DW, Lee K, Kim YS, Oh HY, Cho YH, Cha CJ. Colistin-degrading proteases confer collective resistance to microbial communities during polymicrobial infections. Microbiome 2022; 10:129. [PMID: 35982474 PMCID: PMC9389796 DOI: 10.1186/s40168-022-01315-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/19/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND The increasing prevalence of resistance against the last-resort antibiotic colistin is a significant threat to global public health. Here, we discovered a novel colistin resistance mechanism via enzymatic inactivation of the drug and proposed its clinical importance in microbial communities during polymicrobial infections. RESULTS A bacterial strain of the Gram-negative opportunistic pathogen Stenotrophomonas maltophilia capable of degrading colistin and exhibiting a high-level colistin resistance was isolated from the soil environment. A colistin-degrading protease (Cdp) was identified in this strain, and its contribution to colistin resistance was demonstrated by growth inhibition experiments using knock-out (Δcdp) and complemented (Δcdp::cdp) mutants. Coculture and coinfection experiments revealed that S. maltophilia carrying the cdp gene could inactivate colistin and protect otherwise susceptible Pseudomonas aeruginosa, which may seriously affect the clinical efficacy of the drug for the treatment of cystic fibrosis patients with polymicrobial infection. CONCLUSIONS Our results suggest that Cdp should be recognized as a colistin resistance determinant that confers collective resistance at the microbial community level. Our study will provide vital information for successful clinical outcomes during the treatment of complex polymicrobial infections, particularly including S. maltophilia and other colistin-susceptible Gram-negative pathogens such as P. aeruginosa. Video abstract.
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Affiliation(s)
- Do-Hoon Lee
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17456, Republic of Korea
| | - Ju-Hee Cha
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17456, Republic of Korea
| | - Dae-Wi Kim
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17456, Republic of Korea
- Division of Life Sciences, Jeonbuk National University, Jeonju, 54896, Republic of Korea
| | - Kihyun Lee
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17456, Republic of Korea
| | - Yong-Seok Kim
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17456, Republic of Korea
| | - Hyo-Young Oh
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Seongnam, 13488, Republic of Korea
| | - You-Hee Cho
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Seongnam, 13488, Republic of Korea
| | - Chang-Jun Cha
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17456, Republic of Korea.
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Oh S, Kim Y, Choi D, Park JW, Noh JH, Chung SY, Maeng SK, Cha CJ. Effects of biochar addition on the fate of ciprofloxacin and its associated antibiotic tolerance in an activated sludge microbiome. Environ Pollut 2022; 306:119407. [PMID: 35526648 DOI: 10.1016/j.envpol.2022.119407] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 03/31/2022] [Accepted: 04/30/2022] [Indexed: 06/14/2023]
Abstract
This study investigated the effects of adding biochar (BC) on the fate of ciprofloxacin (CIP) and its related antibiotic tolerance (AT) in activated sludge. Three activated sludge reactors were established with different types of BC, derived from apple, pear, and mulberry tree, respectively, and one reactor with no BC. All reactors were exposed to an environmentally relevant level of CIP that acted as a definitive selective pressure significantly promoting AT to four representative antibiotics (CIP, ampicillin, tetracycline, and polymyxin B) by up to two orders of magnitude. While CIP removal was negligible in the reactor without BC, the BC-dosed reactors effectively removed CIP (70-95% removals) through primarily adsorption by BC and biodegradation/biosorption by biomass. The AT in the BC-added reactors was suppressed by 10-99%, compared to that without BC. The BC addition played a key role in sequestering CIP, thereby decreasing the selective pressure that enabled the proactive prevention of AT increase. 16S rRNA gene sequencing analysis showed that the BC addition alleviated the CIP-mediated toxicity to community diversity and organisms related to phosphorous removal. Machine learning modeling with random forest and support vector models using AS microbiome data collectively pinpointed Achromobacter selected by CIP and strongly associated with the AT increase in activated sludge. The identification of Achromobacter as an important AT bacteria revealed by the machine learning modeling with multiple models was also validated with a linear Pearson's correlation analysis. Overall, our study highlighted Achromobacter as a potential useful sentinel for monitoring AT occurring in the environment and suggested BC as a promising additive in wastewater treatment to improve micropollutant removal, mitigate potential AT propagation, and maintain community diversity against toxic antibiotic loadings.
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Affiliation(s)
- Seungdae Oh
- Department of Civil Engineering, Kyung Hee University, 1732 Deogyeong-daero, Yongin-si, Gyeonggi-do, 17104, Republic of Korea.
| | - Youngjun Kim
- Department of Civil Engineering, Kyung Hee University, 1732 Deogyeong-daero, Yongin-si, Gyeonggi-do, 17104, Republic of Korea
| | - Donggeon Choi
- Department of Civil Engineering, Kyung Hee University, 1732 Deogyeong-daero, Yongin-si, Gyeonggi-do, 17104, Republic of Korea
| | - Ji Won Park
- Department of Civil and Environmental Engineering, Sejong University, 209 Neungdong-ro, Gwangjin-gu, Seoul, 05006, Republic of Korea
| | - Jin Hyung Noh
- Department of Civil and Environmental Engineering, Sejong University, 209 Neungdong-ro, Gwangjin-gu, Seoul, 05006, Republic of Korea
| | - Sang-Yeop Chung
- Department of Civil and Environmental Engineering, Sejong University, 209 Neungdong-ro, Gwangjin-gu, Seoul, 05006, Republic of Korea
| | - Sung Kyu Maeng
- Department of Civil and Environmental Engineering, Sejong University, 209 Neungdong-ro, Gwangjin-gu, Seoul, 05006, Republic of Korea
| | - Chang-Jun Cha
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, 4726 Seodong-daero, Anseong-si, Gyeonggi-do, 17546, Republic of Korea
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Abstract
A Gram-stain-negative, aerobic and motile bacterial strain, designated CJ34T, was isolated from Han River water in the Republic of Korea. Strain CJ34T grew optimally on tryptic soy agar at 30 °C and pH 7.0 in the absence of NaCl. Results of phylogenetic analysis based on 16S rRNA gene sequence showed that strain CJ34T belonged to the genus Comamonas within the family Comamonadaceae and was most closely related to Comamonas testosteroni ATCC 11996T and Comamonas thiooxydans DSM 17888T (both 98.63 % similarity). The average nucleotide identity values between strain CJ34T and two closely related type strains C. testosteroni ATCC 11996T and C. thiooxydans DSM 17888T were 82.77 and 82.73 %, respectively. The major isoprenoid quinone of strain CJ34T was ubiquinone Q-8. The major cellular fatty acids of strain CJ34T were C16 : 0, C16 : 1 ω6c and/or C16 : 1 ω7c and C18 : 1 ω6c and/or C18 : 1 ω7c. The predominant polar lipids of strain CJ34T were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid. Whole genome sequencing revealed that strain CJ34T had a genome of 4.9 Mbp and the G+C content of the genomic DNA was 59.73 mol%. On the basis of the results of this polyphasic taxonomy study, strain CJ34T represents a novel species in the genus Comamonas, for which the name Comamonas fluminis sp. nov. is proposed. The type strain is CJ34T (=KACC 22237T=JCM 34454T).
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Affiliation(s)
- Eun-Hee Park
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Yong-Seok Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Chang-Jun Cha
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
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Chau LTT, Kim YS, Cha CJ. Pedobacter aquae sp. nov., a multi-drug resistant bacterium isolated from fresh water. Antonie van Leeuwenhoek 2022; 115:445-457. [DOI: 10.1007/s10482-022-01708-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 01/11/2022] [Indexed: 12/01/2022]
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11
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Cha JH, Hong M, Cha CJ. Fungal β-Glycosidase Belonging to Subfamily 4 of Glycoside Hydrolase Family 30 with Transglycosylation Activity. J Agric Food Chem 2021; 69:15261-15267. [PMID: 34879649 DOI: 10.1021/acs.jafc.1c05197] [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: 06/13/2023]
Abstract
Fomitopsis palustris, a prominent wood decayer, is known to produce a variety of glycoside hydrolases (GHs). In this study, we characterized a fungal β-glycosidase belonging to subfamily 4 of GH family 30 (GH30). The recombinant protein (FpGH30) showed the highest hydrolytic activity toward p-nitrophenyl-β-d-fucopyranoside (pNPβFuc), followed by p-nitrophenyl-α-l-arabinopyranoside (pNPαAra) and p-nitrophenyl-β-d-galactopyranoside (pNPβGal). FpGH30 also exhibited transglycosylation activities, which catalyzed the transfer of glycosyl moieties to different glycosides and alkyl alcohols. When pNPβFuc, pNPβGal, and pNPαAra were used as substrates, self-condensation reactions occurred, leading to the production of the corresponding transglycosylated products with yields of 21, 26, and 25%, respectively. The enzyme was also able to catalyze the transfucosylation of pNP derivatives of β-d-glucose, β-d-mannose, and β-d-xylose and alkyl alcohols (C1-C6), producing the corresponding transfucosylated products and alkyl fucosides. Our study indicates that FpGH30 is the first characterized fungal β-glycosidase belonging to subfamily 4 of GH30 with transglycosylation activities.
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Affiliation(s)
- Ju-Hee Cha
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Minsun Hong
- Division of Biological Science and Technology, Yonsei University, Wonju 26493, Republic of Korea
| | - Chang-Jun Cha
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
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Borsetto C, Raguideau S, Travis E, Kim DW, Lee DH, Bottrill A, Stark R, Song L, Cha CJ, Pearson J, Quince C, Singer AC, Wellington EMH. Impact of sulfamethoxazole on a riverine microbiome. Water Res 2021; 201:117382. [PMID: 34225233 DOI: 10.1016/j.watres.2021.117382] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 02/09/2021] [Revised: 05/24/2021] [Accepted: 06/19/2021] [Indexed: 06/13/2023]
Abstract
The continued emergence of bacterial pathogens presenting antimicrobial resistance is widely recognised as a global health threat and recent attention focused on potential environmental reservoirs of antibiotic resistance genes (ARGs). Freshwater environments such as rivers represent a potential hotspot for ARGs and antibiotic resistant bacteria as they are receiving systems for effluent discharges from wastewater treatment plants (WWTPs). Effluent also contains low levels of different antimicrobials including antibiotics and biocides. Sulfonamides are antibacterial chemicals widely used in clinical, veterinary and agricultural settings and are frequently detected in sewage sludge and manure in addition to riverine ecosystems. The impact of such exposure on ARG prevalence and diversity is unknown, so the aim of this study was to investigate the release of a sub-lethal concentration of the sulfonamide compound sulfamethoxazole (SMX) on the river bacterial microbiome using a flume system. This system was a semi-natural in vitro flume using river water (30 L) and sediment (6 kg) with circulation to mimic river flow. A combination of 'omics' approaches were conducted to study the impact of SMX exposure on the microbiomes within the flumes. Metagenomic analysis showed that the addition of low concentrations of SMX (<4 μg L-1) had a limited effect on the bacterial resistome in the water fraction only, with no impact observed in the sediment. Metaproteomics did not show differences in ARGs expression with SMX exposure in water. Overall, the river bacterial community was resilient to short term exposure to sub-lethal concentrations of SMX which mimics the exposure such communities experience downstream of WWTPs throughout the year.
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Affiliation(s)
- Chiara Borsetto
- University of Warwick, School of Life Sciences, Coventry, UK.
| | | | - Emma Travis
- University of Warwick, School of Life Sciences, Coventry, UK
| | - Dae-Wi Kim
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, Republic of Korea
| | - Do-Hoon Lee
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, Republic of Korea
| | - Andrew Bottrill
- University of Warwick, School of Life Sciences, Coventry, UK
| | - Richard Stark
- University of Warwick, School of Life Sciences, Coventry, UK
| | - Lijiang Song
- University of Warwick, Department of Chemistry, Coventry, UK
| | - Chang-Jun Cha
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, Republic of Korea
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13
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Abstract
A Gram-stain-negative, aerobic, short rod-shaped, pale yellow-pigmented, non-motile and gentamycin-resistant bacterial strain designated CJ210T was isolated from the Han River, Republic of Korea. Strain CJ210T grew optimally at 30 °C and pH 7.0 in the absence of NaCl on tryptic soy agar. Flexirubin-type pigments were not produced. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strain CJ210T belonged to the genus Myroides within the family Flavobacteriaceae and was most closely related to Myroides odoratus KACC 14347T (98.1 % similarity), followed by M. injenensis KCTC 23367T (95.3 % similarity). The average nucleotide identity values between strain CJ210T and two closely related type strains M. odoratus KACC 14347T and M. injenensis KCTC 23367T were 83.7 and 73.8 %, respectively. The digital DNA-DNA hybridization results between strain CJ210T and the related type strains were 27.5 and 20.2 %, respectively. Strain CJ210T contained menaquinone 6 (MK-6) as the predominant menaquinone. The predominant polar lipids were phosphatidylethanolamine, two unidentified aminolipids and two unidentified lipids. The major fatty acids of strain CJ210T were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 9 (comprising iso-C17 : 1 ω9c and/or C16 : 0 10-methyl). Whole genome sequencing revealed that strain CJ210T had a genome of 3.8 Mbp with 36.5 % DNA G+C content. The genome contained several antimicrobial resistance genes including an aminoglycoside-resistant gene. On the basis of the polyphasic taxonomic study, strain CJ210T represents a novel species in the genus Myroides, for which name Myrodies fluvii sp. nov. is proposed. The type strain is CJ210T (=KACC 19954T=JCM 33306T).
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Affiliation(s)
- Yong-Seok Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Seo-Hyeon Jang
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Chang-Jun Cha
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
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14
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Kim DW, Cha CJ. Antibiotic resistome from the One-Health perspective: understanding and controlling antimicrobial resistance transmission. Exp Mol Med 2021; 53:301-309. [PMID: 33642573 PMCID: PMC8080597 DOI: 10.1038/s12276-021-00569-z] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [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: 11/04/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 01/31/2023] Open
Abstract
The concept of the antibiotic resistome was introduced just over a decade ago, and since then, active resistome studies have been conducted. In the present study, we describe the previously established concept of the resistome, which encompasses all types of antibiotic resistance genes (ARGs), and the important findings from each One-Health sector considering this concept, thereby emphasizing the significance of the One-Health approach in understanding ARG transmission. Cutting-edge research methodologies are essential for deciphering the complex resistome structure in the microbiomes of humans, animals, and the environment. Based on the recent achievements of resistome studies in multiple One-Health sectors, future directions for resistome research have been suggested to improve the understanding and control of ARG transmission: (1) ranking the critical ARGs and their hosts; (2) understanding ARG transmission at the interfaces of One-Health sectors; (3) identifying selective pressures affecting the emergence, transmission, and evolution of ARGs; and (4) elucidating the mechanisms that allow an organism to overcome taxonomic barriers in ARG transmission.
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Affiliation(s)
- Dae-Wi Kim
- grid.411545.00000 0004 0470 4320Division of Life Sciences, Jeonbuk National University, Jeonju, 54896 Republic of Korea
| | - Chang-Jun Cha
- grid.254224.70000 0001 0789 9563Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546 Republic of Korea
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Redhead S, Nieuwland J, Esteves S, Lee DH, Kim DW, Mathias J, Cha CJ, Toleman M, Dinsdale R, Guwy A, Hayhurst E. Fate of antibiotic resistant E. coli and antibiotic resistance genes during full scale conventional and advanced anaerobic digestion of sewage sludge. PLoS One 2020; 15:e0237283. [PMID: 33259486 PMCID: PMC7707479 DOI: 10.1371/journal.pone.0237283] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 11/10/2020] [Indexed: 11/19/2022] Open
Abstract
Antibiotic resistant bacteria (ARB) and their genes (ARGs) have become recognised as significant emerging environmental pollutants. ARB and ARGs in sewage sludge can be transmitted back to humans via the food chain when sludge is recycled to agricultural land, making sludge treatment key to control the release of ARB and ARGs to the environment. This study investigated the fate of antibiotic resistant Escherichia coli and a large set of antibiotic resistance genes (ARGs) during full scale anaerobic digestion (AD) of sewage sludge at two U.K. wastewater treatment plants and evaluated the impact of thermal hydrolysis (TH) pre-treatment on their abundance and diversity. Absolute abundance of 13 ARGs and the Class I integron gene intI1 was calculated using single gene quantitative (q) PCR. High through-put qPCR analysis was also used to determine the relative abundance of 370 ARGs and mobile genetic elements (MGEs). Results revealed that TH reduced the absolute abundance of all ARGs tested and intI1 by 10-12,000 fold. After subsequent AD, a rebound effect was seen in many ARGs. The fate of ARGs during AD without pre-treatment was variable. Relative abundance of most ARGs and MGEs decreased or fluctuated, with the exception of macrolide resistance genes, which were enriched at both plants, and tetracyline and glycopeptide resistance genes which were enriched in the plant employing TH. Diversity of ARGs and MGEs decreased in both plants during sludge treatment. Principal coordinates analysis revealed that ARGs are clearly distinguished according to treatment step, whereas MGEs in digested sludge cluster according to site. This study provides a comprehensive within-digestor analysis of the fate of ARGs, MGEs and antibiotic resistant E. coli and highlights the effectiveness of AD, particularly when TH is used as a pre-treatment, at reducing the abundance of most ARGs and MGEs in sludgeand preventing their release into the environment.
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Affiliation(s)
- Sky Redhead
- Faculty of Computing, Engineering and Science, University of South Wales, Pontypridd, United Kingdom
| | - Jeroen Nieuwland
- Faculty of Computing, Engineering and Science, University of South Wales, Pontypridd, United Kingdom
| | - Sandra Esteves
- Faculty of Computing, Engineering and Science, University of South Wales, Pontypridd, United Kingdom
| | - Do-Hoon Lee
- Department of Systems Biotechnology and Centre for Antibiotic Resistome, College of Biotechnology & Natural Resources, Chung-Ang University, Anseong, Republic of Korea
| | - Dae-Wi Kim
- Department of Systems Biotechnology and Centre for Antibiotic Resistome, College of Biotechnology & Natural Resources, Chung-Ang University, Anseong, Republic of Korea
| | - Jordan Mathias
- School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Chang-Jun Cha
- Department of Systems Biotechnology and Centre for Antibiotic Resistome, College of Biotechnology & Natural Resources, Chung-Ang University, Anseong, Republic of Korea
| | - Mark Toleman
- School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Richard Dinsdale
- Faculty of Computing, Engineering and Science, University of South Wales, Pontypridd, United Kingdom
| | - Alan Guwy
- Faculty of Computing, Engineering and Science, University of South Wales, Pontypridd, United Kingdom
| | - Emma Hayhurst
- Faculty of Computing, Engineering and Science, University of South Wales, Pontypridd, United Kingdom
- * E-mail:
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Moon K, Jeon JH, Kang I, Park KS, Lee K, Cha CJ, Lee SH, Cho JC. Freshwater viral metagenome reveals novel and functional phage-borne antibiotic resistance genes. Microbiome 2020; 8:75. [PMID: 32482165 PMCID: PMC7265639 DOI: 10.1186/s40168-020-00863-4] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/11/2020] [Indexed: 05/20/2023]
Abstract
BACKGROUND Antibiotic resistance developed by bacteria is a significant threat to global health. Antibiotic resistance genes (ARGs) spread across different bacterial populations through multiple dissemination routes, including horizontal gene transfer mediated by bacteriophages. ARGs carried by bacteriophages are considered especially threatening due to their prolonged persistence in the environment, fast replication rates, and ability to infect diverse bacterial hosts. Several studies employing qPCR and viral metagenomics have shown that viral fraction and viral sequence reads in clinical and environmental samples carry many ARGs. However, only a few ARGs have been found in viral contigs assembled from metagenome reads, with most of these genes lacking effective antibiotic resistance phenotypes. Owing to the wide application of viral metagenomics, nevertheless, different classes of ARGs are being continuously found in viral metagenomes acquired from diverse environments. As such, the presence and functionality of ARGs encoded by bacteriophages remain up for debate. RESULTS We evaluated ARGs excavated from viral contigs recovered from urban surface water viral metagenome data. In virome reads and contigs, diverse ARGs, including polymyxin resistance genes, multidrug efflux proteins, and β-lactamases, were identified. In particular, when a lenient threshold of e value of ≤ 1 × e-5 and query coverage of ≥ 60% were employed in the Resfams database, the novel β-lactamases blaHRV-1 and blaHRVM-1 were found. These genes had unique sequences, forming distinct clades of class A and subclass B3 β-lactamases, respectively. Minimum inhibitory concentration analyses for E. coli strains harboring blaHRV-1 and blaHRVM-1 and catalytic kinetics of purified HRV-1 and HRVM-1 showed reduced susceptibility to penicillin, narrow- and extended-spectrum cephalosporins, and carbapenems. These genes were also found in bacterial metagenomes, indicating that they were harbored by actively infecting phages. CONCLUSION Our results showed that viruses in the environment carry as-yet-unreported functional ARGs, albeit in small quantities. We thereby suggest that environmental bacteriophages could be reservoirs of widely variable, unknown ARGs that could be disseminated via virus-host interactions. Video abstract.
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Affiliation(s)
- Kira Moon
- Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea
| | - Jeong Ho Jeon
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, 116 Myongjiro, Yongin, Gyeonggi-do, 17058, Republic of Korea
| | - Ilnam Kang
- Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea
| | - Kwang Seung Park
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, 116 Myongjiro, Yongin, Gyeonggi-do, 17058, Republic of Korea
| | - Kihyun Lee
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea
| | - Chang-Jun Cha
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea
| | - Sang Hee Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, 116 Myongjiro, Yongin, Gyeonggi-do, 17058, Republic of Korea.
| | - Jang-Cheon Cho
- Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea.
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Lee K, Kim DW, Lee DH, Kim YS, Bu JH, Cha JH, Thawng CN, Hwang EM, Seong HJ, Sul WJ, Wellington EMH, Quince C, Cha CJ. Mobile resistome of human gut and pathogen drives anthropogenic bloom of antibiotic resistance. Microbiome 2020; 8:2. [PMID: 31910889 PMCID: PMC6947943 DOI: 10.1186/s40168-019-0774-7] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 12/09/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND The impact of human activities on the environmental resistome has been documented in many studies, but there remains the controversial question of whether the increased antibiotic resistance observed in anthropogenically impacted environments is just a result of contamination by resistant fecal microbes or is mediated by indigenous environmental organisms. Here, to determine exactly how anthropogenic influences shape the environmental resistome, we resolved the microbiome, resistome, and mobilome of the planktonic microbial communities along a single river, the Han, which spans a gradient of human activities. RESULTS The bloom of antibiotic resistance genes (ARGs) was evident in the downstream regions and distinct successional dynamics of the river resistome occurred across the spatial continuum. We identified a number of widespread ARG sequences shared between the river, human gut, and pathogenic bacteria. These human-related ARGs were largely associated with mobile genetic elements rather than particular gut taxa and mainly responsible for anthropogenically driven bloom of the downstream river resistome. Furthermore, both sequence- and phenotype-based analyses revealed environmental relatives of clinically important proteobacteria as major carriers of these ARGs. CONCLUSIONS Our results demonstrate a more nuanced view of the impact of anthropogenic activities on the river resistome: fecal contamination is present and allows the transmission of ARGs to the environmental resistome, but these mobile genes rather than resistant fecal bacteria proliferate in environmental relatives of their original hosts. Video abstract.
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Affiliation(s)
- Kihyun Lee
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Dae-Wi Kim
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Do-Hoon Lee
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Yong-Seok Kim
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Ji-Hye Bu
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Ju-Hee Cha
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Cung Nawl Thawng
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Eun-Mi Hwang
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Hoon Je Seong
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Woo Jun Sul
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
| | | | | | - Chang-Jun Cha
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea.
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Kim DW, Thawng CN, Lee K, Wellington EMH, Cha CJ. A novel sulfonamide resistance mechanism by two-component flavin-dependent monooxygenase system in sulfonamide-degrading actinobacteria. Environ Int 2019; 127:206-215. [PMID: 30928844 DOI: 10.1016/j.envint.2019.03.046] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [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: 01/23/2019] [Revised: 03/18/2019] [Accepted: 03/19/2019] [Indexed: 05/19/2023]
Abstract
Sulfonamide-degrading bacteria have been discovered in various environments, suggesting the presence of novel resistance mechanisms via drug inactivation. In this study, Microbacterium sp. CJ77 capable of utilizing various sulfonamides as a sole carbon source was isolated from a composting facility. Genome and proteome analyses revealed that a gene cluster containing a flavin-dependent monooxygenase and a flavin reductase was highly up-regulated in response to sulfonamides. Biochemical analysis showed that the two-component monooxygenase system was key enzymes for the initial cleavage of sulfonamides. Co-expression of the two-component system in Escherichia coli conferred decreased susceptibility to sulfamethoxazole, indicating that the genes encoding drug-inactivating enzymes are potential resistance determinants. Comparative genomic analysis revealed that the gene cluster containing sulfonamide monooxygenase (renamed as sulX) and flavin reductase (sulR) was highly conserved in a genomic island shared among sulfonamide-degrading actinobacteria, all of which also contained sul1-carrying class 1 integrons. These results suggest that the sulfonamide metabolism may have evolved in sulfonamide-resistant bacteria which had already acquired the class 1 integron under sulfonamide selection pressures. Furthermore, the presence of multiple insertion sequence elements and putative composite transposon structures containing the sulX gene cluster indicated potential mobilization. This is the first study to report that sulX responsible for both sulfonamide degradation and resistance is prevalent in sulfonamide-degrading actinobacteria and its genetic signatures indicate horizontal gene transfer of the novel resistance gene.
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Affiliation(s)
- Dae-Wi Kim
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong 17456, Republic of Korea
| | - Cung Nawl Thawng
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong 17456, Republic of Korea
| | - Kihyun Lee
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong 17456, Republic of Korea
| | | | - Chang-Jun Cha
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong 17456, Republic of Korea.
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Abstract
A Gram-stain-negative, yellow-pigmented, non-motile, non-spore-forming, aerobic and rod-shaped bacterial strain, designated 17S1E7T, was isolated from the Han River, Republic of Korea, and characterized by polyphasic taxonomy analyses. Strain 17S1E7T grew optimally on tryptic soy agar at 37 °C and pH 7.0 in the absence of NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain 17S1E7T belonged to the genus Chryseobacterium and was most closely related to Chryseobacterium culicis DSM 23031T (98.54 %). The average nucleotide identity value of strain 17S1E7T was 91.1 % to Chryseobacterium culicis DSM 23031T, which was lower than the cut-off of 95-96 %. The DNA G+C content of strain 17S1E7T was 37.4 mol%. Flexirubin-type pigments were produced. The predominant respiratory quinone was menaquinone 6. The major fatty acids of strain 17S1E7T were iso-C15 : 0, summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl), iso-C17 : 0 3-OH and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c). The predominant polar lipid was phosphatidylethanolamine. Based on polyphasic taxonomy data, strain 17S1E7T represents a novel species of the genus Chryseobacterium, for which the name Chryseobacterium aureum sp. nov. is proposed. The type strain is 17S1E7T (=KACC 19920T=JCM 33165T).
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Affiliation(s)
- Ju-Eun Lee
- 1Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Eun-Mi Hwang
- 2Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Chang-Jun Cha
- 2Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Geun-Bae Kim
- 1Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Republic of Korea
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Oh S, Choi D, Cha CJ. Ecological processes underpinning microbial community structure during exposure to subinhibitory level of triclosan. Sci Rep 2019; 9:4598. [PMID: 30872712 PMCID: PMC6418085 DOI: 10.1038/s41598-019-40936-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 02/21/2019] [Indexed: 11/30/2022] Open
Abstract
Ecological processes shaping the structure and diversity of microbial communities are of practical importance for managing the function and resilience of engineered biological ecosystems such as activated sludge processes. This study systematically evaluated the ecological processes acting during continuous exposure to a subinhibitory level of antimicrobial triclosan (TCS) as an environmental stressor. 16S rRNA gene-based community profiling revealed significant perturbations on the community structure and dramatic reduction (by 20-30%) in species diversity/richness compared to those under the control conditions. In addition, community profiling determined the prevalence of the deterministic processes overwhelming the ecological stochasticity. Analysis of both community composition and phenotypes in the TCS-exposed communities suggested the detailed deterministic mechanism: selection of TCS degrading (Sphingopyxis) and resistant (Pseudoxanthomonas) bacterial populations. The analysis also revealed a significant reduction of core activated sludge members, Chitinophagaceae (e.g., Ferruginibacter) and Comamonadaceae (e.g., Acidovorax), potentially affecting ecosystem functions (e.g., floc formation and nutrient removal) directly associated with system performance (i.e., wastewater treatment efficiency and effluent quality). Overall, our study provides new findings that inform the mechanisms underlying the community structure and diversity of activated sludge, which not only advances the current understanding of microbial ecology in activated sludge, but also has practical implications for the design and operation of environmental bioprocesses for treatment of antimicrobial-bearing waste streams.
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Affiliation(s)
- Seungdae Oh
- Department of Civil Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do, Republic of Korea.
| | - Donggeon Choi
- Department of Civil Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Chang-Jun Cha
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, Gyeonggi-do, Republic of Korea
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21
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Kim DW, Lee K, Lee DH, Cha CJ. Comparative genomic analysis of pyrene-degrading Mycobacterium species: Genomic islands and ring-hydroxylating dioxygenases involved in pyrene degradation. J Microbiol 2018; 56:798-804. [DOI: 10.1007/s12275-018-8372-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/09/2018] [Accepted: 08/13/2018] [Indexed: 10/28/2022]
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Kim DW, Thawng CN, Lee K, Cha CJ. Revisiting Polymorphic Diversity of Aminoglycoside N-Acetyltransferase AAC(6')-Ib Based on Bacterial Genomes of Human, Animal, and Environmental Origins. Front Microbiol 2018; 9:1831. [PMID: 30147681 PMCID: PMC6095969 DOI: 10.3389/fmicb.2018.01831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 05/30/2018] [Accepted: 07/23/2018] [Indexed: 12/20/2022] Open
Abstract
The prevalence of aac(6')-Ib variants has been demonstrated in numerous epidemiological studies. We revisited the polymorphic diversity of aminoglycoside 6'-N-acetyltransferase gene [aac(6')-Ib] in the bacterial genome databases based on One Health perspectives. aac(6')-Ib was searched against bacterial complete and draft genome databases of NCBI. Based on the major polymorphic residues 102, 117, and 179, taxonomy, ecology, and temporal emergence of bacterial isolates harboring variants of aac(6')-Ib gene were evaluated using whole-genome sequences available in the databases. A total of 3,964 aac(6')-Ib sequences were found to be present in the genomes of 34 bacterial genera, mostly found in Gammaproteobacteria. Among these, aac(6')-Ib-cr variant, known to confer fluoroquinolone resistance, were increasingly detected in bacterial genomes and most abundant in the genera Klebsiella and Escherichia, thereby suggesting that these genera were the major reservoirs of the plasmid-mediated quinolone resistance (PMQR) determinant. The proportions of the cr variant were higher in animal and environmental isolates than in human isolates, among which the variant was dominant (>50%) in the genomes of intestinal, rectal, and fecal origins. In addition, our study suggested that the prevalence of the cr variant was associated with the occurrence of a variant with the mutation L117 (IbL). An integrated surveillance system for antimicrobial resistance in human, animal, and environmental sectors, based on whole-genome sequencing, would provide a better insight into the evolution, ecology, and epidemiology of antimicrobial-resistant bacteria.
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Affiliation(s)
| | | | | | - Chang-Jun Cha
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, South Korea
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Cha JH, Yoon JJ, Cha CJ. Functional characterization of a thermostable endoglucanase belonging to glycoside hydrolase family 45 from Fomitopsis palustris. Appl Microbiol Biotechnol 2018; 102:6515-6523. [DOI: 10.1007/s00253-018-9075-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 05/03/2018] [Accepted: 05/06/2018] [Indexed: 11/25/2022]
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Affiliation(s)
- Yong-Seok Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Chang-Jun Cha
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
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25
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Affiliation(s)
- Ji-Hye Bu
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Chang-Jun Cha
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
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Affiliation(s)
- Shamsun Nahar
- Department of Systems Biotechnology, Chung-Ang University, Anseong 456-756, Republic of Korea
| | - Chang-Jun Cha
- Department of Systems Biotechnology, Chung-Ang University, Anseong 456-756, Republic of Korea
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Lee CR, Lee JH, Park KS, Jeon JH, Kim YB, Cha CJ, Jeong BC, Lee SH. Antimicrobial Resistance of Hypervirulent Klebsiella pneumoniae: Epidemiology, Hypervirulence-Associated Determinants, and Resistance Mechanisms. Front Cell Infect Microbiol 2017; 7:483. [PMID: 29209595 PMCID: PMC5702448 DOI: 10.3389/fcimb.2017.00483] [Citation(s) in RCA: 253] [Impact Index Per Article: 36.1] [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: 07/19/2017] [Accepted: 11/09/2017] [Indexed: 01/09/2023] Open
Abstract
Klebsiella pneumoniae is one of the most clinically relevant species in immunocompromised individuals responsible for community-acquired and nosocomial infections, including pneumonias, urinary tract infections, bacteremias, and liver abscesses. Since the mid-1980s, hypervirulent K. pneumoniae, generally associated with the hypermucoviscosity phenotype, has emerged as a clinically significant pathogen responsible for serious disseminated infections, such as pyogenic liver abscesses, osteomyelitis, and endophthalmitis, in a generally younger and healthier population. Hypervirulent K. pneumoniae infections were primarily found in East Asia and now are increasingly being reported worldwide. Although most hypervirulent K. pneumoniae isolates are antibiotic-susceptible, some isolates with combined virulence and resistance, such as the carbapenem-resistant hypervirulent K. pneumoniae isolates, are increasingly being detected. The combination of multidrug resistance and enhanced virulence has the potential to cause the next clinical crisis. To better understand the basic biology of hypervirulent K. pneumoniae, this review will provide a summarization and discussion focused on epidemiology, hypervirulence-associated factors, and antibiotic resistance mechanisms of such hypervirulent strains. Epidemiological analysis of recent clinical isolates in China warns the global dissemination of hypervirulent K. pneumoniae strains with extensive antibiotic resistance in the near future. Therefore, an immediate response to recognize the global dissemination of this hypervirulent strain with resistance determinants is an urgent priority.
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Affiliation(s)
- Chang-Ro Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, South Korea
| | - Jung Hun Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, South Korea
| | - Kwang Seung Park
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, South Korea
| | - Jeong Ho Jeon
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, South Korea
| | - Young Bae Kim
- Biotechnology Program, North Shore Community College, Danvers, MA, United States
| | - Chang-Jun Cha
- Department of Systems Biotechnology, College of Biotechnology and Natural Resources, Chung-Ang University, Anseong, South Korea
| | - Byeong Chul Jeong
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, South Korea
| | - Sang Hee Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, South Korea
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Lee DH, Cha CJ. Ramlibacter alkalitolerans sp. nov., alkali-tolerant bacterium isolated from soil of ginseng. Int J Syst Evol Microbiol 2017; 67:4619-4623. [DOI: 10.1099/ijsem.0.002342] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Do-Hoon Lee
- Department of Systems Biotechnology, Chung-Ang University, Anseong 456-756, Republic of Korea
| | - Chang-Jun Cha
- Department of Systems Biotechnology, Chung-Ang University, Anseong 456-756, Republic of Korea
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Lee CR, Lee JH, Park M, Park KS, Bae IK, Kim YB, Cha CJ, Jeong BC, Lee SH. Biology of Acinetobacter baumannii: Pathogenesis, Antibiotic Resistance Mechanisms, and Prospective Treatment Options. Front Cell Infect Microbiol 2017; 7:55. [PMID: 28348979 PMCID: PMC5346588 DOI: 10.3389/fcimb.2017.00055] [Citation(s) in RCA: 477] [Impact Index Per Article: 68.1] [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: 12/19/2016] [Accepted: 02/13/2017] [Indexed: 12/27/2022] Open
Abstract
Acinetobacter baumannii is undoubtedly one of the most successful pathogens responsible for hospital-acquired nosocomial infections in the modern healthcare system. Due to the prevalence of infections and outbreaks caused by multi-drug resistant A. baumannii, few antibiotics are effective for treating infections caused by this pathogen. To overcome this problem, knowledge of the pathogenesis and antibiotic resistance mechanisms of A. baumannii is important. In this review, we summarize current studies on the virulence factors that contribute to A. baumannii pathogenesis, including porins, capsular polysaccharides, lipopolysaccharides, phospholipases, outer membrane vesicles, metal acquisition systems, and protein secretion systems. Mechanisms of antibiotic resistance of this organism, including acquirement of β-lactamases, up-regulation of multidrug efflux pumps, modification of aminoglycosides, permeability defects, and alteration of target sites, are also discussed. Lastly, novel prospective treatment options for infections caused by multi-drug resistant A. baumannii are summarized.
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Affiliation(s)
- Chang-Ro Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University Yongin, South Korea
| | - Jung Hun Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University Yongin, South Korea
| | - Moonhee Park
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji UniversityYongin, South Korea; DNA Analysis Division, Seoul Institute, National Forensic ServiceSeoul, South Korea
| | - Kwang Seung Park
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University Yongin, South Korea
| | - Il Kwon Bae
- Department of Dental Hygiene, College of Health and Welfare, Silla University Busan, South Korea
| | - Young Bae Kim
- Biotechnology Program, North Shore Community College Danvers, MA, USA
| | - Chang-Jun Cha
- Department of Systems Biotechnology, College of Biotechnology and Natural Resources, Chung-Ang University Anseong, South Korea
| | - Byeong Chul Jeong
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University Yongin, South Korea
| | - Sang Hee Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University Yongin, South Korea
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30
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Affiliation(s)
- Do-Hoon Lee
- Department of Systems Biotechnology, Chung-Ang University, Anseong 456-756, Republic of Korea
| | - Chang-Jun Cha
- Department of Systems Biotechnology, Chung-Ang University, Anseong 456-756, Republic of Korea
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Kim E, Choi S, Bae JW, Cha CJ, Im WT, Jahng KY, Joh KS, Yi H. A report of 10 unrecorded bacterial species of Korea, belonging to the phylum Firmicutes. ACTA ACUST UNITED AC 2016. [DOI: 10.12651/jsr.2016.5.2.235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Abstract
A novel bacterial strain, CJ22T, was isolated from soil of a ginseng field located in Anseong, Korea. Cells of strain CJ22T were aerobic, Gram-stain-positive, endospore-forming, motile, oxidase- and catalase-positive and rod-shaped. The isolate grew optimally at pH 7 and 30 °C. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain CJ22T belonged to the genus Cohnella, displaying highest sequence similarity of 97.3% with Cohnella panacarvi Gsoil 349T. DNA-DNA relatedness between strain CJ22T and its closest relative was 35.5 % (reciprocal value, 23.8%). The phenotypic features of strain CJ22T also distinguished it from related species of the genus Cohnella. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major isoprenoid quinone was menaquinone MK-7 and the major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, lysyl-phosphatidylglycerol, two unidentified phospholipids and two unidentified aminophospholipids. The predominant cellular fatty acids of strain CJ22T were anteiso-C15 : 0, iso-C16:0 and C16:0. The DNA G+C content was 63.1 mol%. Based on data from this polyphasic taxonomic study, strain CJ22T is considered to represent a novel species of the genus Cohnella, for which the name Cohnella saccharovorans sp. nov. is proposed. The type strain is CJ22T (=KACC 17501T=JCM 19227T).
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Affiliation(s)
- Jung-Hye Choi
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Ji-Hye Seok
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Ho-Jin Jang
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Ju-Hee Cha
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Chang-Jun Cha
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
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Unno T, Choi JH, Hur HG, Sadowsky MJ, Ahn YT, Huh CS, Kim GB, Cha CJ. Changes in human gut microbiota influenced by probiotic fermented milk ingestion. J Dairy Sci 2015; 98:3568-76. [PMID: 25864056 DOI: 10.3168/jds.2014-8943] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [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: 10/06/2014] [Accepted: 03/11/2015] [Indexed: 12/29/2022]
Abstract
We investigated the effect of consuming probiotic fermented milk (PFM) on the microbial community structure in the human intestinal tract by using high-throughput barcoded pyrosequencing. Six healthy adults ingested 2 servings of PFM daily for 3 wk, and their fecal microbiota were analyzed before and after 3 wk of PFM ingestion period and for another 3 wk following the termination of PFM ingestion (the noningestion period). Fecal microbial communities were characterized by sequencing of the V1-V3 hypervariable regions of the 16S rRNA gene. All subjects showed a similar pattern of microbiota at the phylum level, where the relative abundance of Bacteriodetes species increased during the PFM ingestion period and decreased during the noningestion period. The increase in Bacteroidetes was found to be due to an increase in members of the families Bacteroidaceae or Prevotellaceae. In contrast to PFM-induced adaptation at the phylum level, the taxonomic composition at the genus level showed a considerable alteration in fecal microbiota induced by PFM ingestion. As revealed by analysis of operational taxonomic units (OTU), the numbers of shared OTU were low among the 3 different treatments (before, during, and after PFM ingestion), but the abundance of the shared OTU was relatively high, indicating that the majority (>77.8%) of total microbiota was maintained by shared OTU during PFM ingestion and after its termination. Our results suggest that PFM consumption could alter microbial community structure in the gastrointestinal tract of adult humans while maintaining the stability of microbiota.
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Affiliation(s)
- Tatsuya Unno
- Faculty of Biotechnology, College of Applied Life Sciences, Jeju National University, Jeju 690-756, Republic of Korea
| | - Jung-Hye Choi
- Department of Systems Biotechnology, Chung-Ang University, Anseong 456-756, Republic of Korea
| | - Hor-Gil Hur
- School of Environmental Science and Engineering, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Michael J Sadowsky
- Department of Soil, Water, and Climate; and BioTechnology Institute, University of Minnesota, St. Paul 55108
| | - Young-Tae Ahn
- R&BD Center, Korea Yakult Co. Ltd., Yongin 446-901, Republic of Korea
| | - Chul-Sung Huh
- Institute of Green Bio Science and Technology, Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 232-916, Republic of Korea
| | - Geun-Bae Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong 456-756, Republic of Korea.
| | - Chang-Jun Cha
- Department of Systems Biotechnology, Chung-Ang University, Anseong 456-756, Republic of Korea.
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Abstract
A novel strain, designated strain CU3-7(T), was isolated from faeces of a two-week-old baby. The isolate was Gram-staining-positive, anaerobic and rod-shaped. Results from 16S rRNA gene sequence analysis revealed that strain CU3-7(T) was phylogenetically affiliated with members of the genus Bifidobacterium. Strain CU3-7(T) showed the highest level of sequence similarity with Bifidobacterium adolescentis KCTC 3216(T) (98.4 %), followed by Bifidobacterium ruminantium KCTC 3425(T) (97.9 %). Analysis of hsp60 sequences showed that strain CU3-7(T) was closely related to B. adolescentis KCTC 3216(T) (94.0 %) and B. ruminantium KCTC 3425(T) (92.5 %). The DNA-DNA hybridization values with the closely related strains were all below the cut-off value for species delineation, 17.0 % with B. ruminantium KCTC 3425(T) and 14.9 % with B. adolescentis KCTC 3216(T). Fructose-6-phosphate phosphoketolase activity was detected. The predominant cellular fatty acids were C16 : 0 (27.7 %), C18 : 1ω9c (27.4 %) and C18 : 1ω9c dimethylacetate (15.5 %). The DNA G+C content was 58.6 mol%. On the basis of polyphasic taxonomy, strain CU3-7(T) should be classified as the type strain of a novel species within the genus Bifidobacterium, for which the name Bifidobacterium faecale sp. nov. is proposed ( = KACC 17904(T) = JCM 19861(T)).
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Affiliation(s)
- Jung-Hye Choi
- Department of Systems Biotechnology, Chung-Ang University, Anseong 456-756, Republic of Korea
| | - Kyung Min Lee
- Department of Animal Science and Technology, Chung-Ang University, Anseong 456-756, Republic of Korea
| | - Myung-Ki Lee
- Fermentation and Functionality Research Group, Korea Food Research Institute, Sungnam 463-746, Republic of Korea
| | - Chang-Jun Cha
- Department of Systems Biotechnology, Chung-Ang University, Anseong 456-756, Republic of Korea
| | - Geun-Bae Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong 456-756, Republic of Korea
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Abstract
Bacterial communities in the different regions of gastrointestinal tract (GIT) of broiler chickens were analyzed by pyrosequencing approach to understand microbial composition and diversity. The DNA samples extracted from 7 different regions along the GIT were subjected to bacterial-community analysis by pyrosequencing of the V1-V3 region of 16S rRNA gene. Major bacterial phyla in the chicken-gut microbiota included Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Acidobacteria, but Firmicutes were mostly dominant (67.3 ± 16.1% of the total sequence reads identified). Among Firmicutes, Lactobacillales, including the genera Lactobacillus and Enterococcus, were the most dominant (51.8 ± 34.5% of the total sequence reads identified) from the crop to ileum. In contrast, in the cecum and large intestine, those genera were rarely detected, and Clostridiales were dominant (55.9 ± 31.4%). Fast UniFrac analysis showed that microbial communities from the crop to jejunum of the same individual chicken were grouped together, and those from ileum, cecum, and large intestine were clustered in a more GIT-specific manner. The numbers of shared operational taxonomic units between the neighboring segments of GIT were low, ranging from 2.9 to 20.3%. However, the abundance of shared operational taxonomic units in each segment was relatively high, ranging from 61.7 to 85.0%, suggesting that substantial proportions of microbial communities were shared between each segment and its neighboring segments, comprising a core microbiota. Our results suggested that the microbial communities of 7 main segments in the chicken GIT were distinctive according to both individuals and the different segments of GIT, but their stability was maintained along the GIT.
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Affiliation(s)
- J H Choi
- Department of Systems Biotechnology, Institute of Microbiomics, and
| | - G B Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong 456-756, Republic of Korea
| | - C J Cha
- Department of Systems Biotechnology, Institute of Microbiomics, and
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Abstract
Background Staphylococcus aureus is a pathogen that causes food poisoning and community-associated infection with antibiotic resistance. This species is an indigenous intestinal microbe found in infants and not found in adult intestine. The relatively small genome size and rapid evolution of antibiotic resistance genes in the species have been drawing an increasing attention in public health. To extend our understanding of the species and use the genome data for comparative genomic studies, we sequenced the type strain of S. aureus subsp. aureus DSM 20231T. Results Seventeen contigs were generated using hybrid assembly of sequences derived from the Roche 454 and Illumina systems. The length of the genome sequence was 2,902,619 bases with a G + C content of 32.8%. Among the 2,550 annotated CDSs, 44 CDSs were annotated to antibiotic resistance genes and 13 CDSs were related to methicillin resistance. It is interesting to note that this strain was first isolated in 1884 before methicillin was generally used on patients. Conclusions The present study analyzed the genome sequence of S. aureus subsp. aureus type strain as the reference sequence for comparative genomic analyses of clinical isolates. Methicillin resistance genes found in the genome indicate the presence of antibiotic resistance mechanism prior to the usage of antibiotics. Further comparative genomic studies of methicillin-resistant strains based on this reference genome would help to understand the evolution of resistance mechanism and dissemination of resistance genes.
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Affiliation(s)
| | | | | | - Chang-Jun Cha
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Republic of Korea.
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Abstract
A Gram-staining-positive, motile, facultatively anaerobic, endospore-forming and rod-shaped bacterium, designated strain CJ32(T), was isolated from ginseng soil at Geumsan in Korea. The isolate grew optimally at 30 °C, 2% (w/v) NaCl and pH 7.0. Colonies of strain CJ32(T) were beige and circular with an entire margin on LB agar plates. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CJ32(T) was associated with the genus Bacillus and was most closely related to Bacillus graminis YC6957(T) (97.3% similarity) and Bacillus lentus IAM 12466(T) (97.1%). DNA-DNA hybridization with closely related strains was below 31.3%. The major respiratory isoprenoid quinone was MK-7. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The polar lipid profile of strain CJ32(T) consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several unidentified lipids, including phospholipids, aminolipids and aminophospholipids. The predominant fatty acids of strain CJ32(T) were iso-C15:0 and anteiso-C15:0. The G+C content of the genomic DNA was 35.1 mol%. Based on phenotypic, genotypic and phylogenetic data, strain CJ32(T) should be classified within a novel species of the genus Bacillus, for which the name Bacillus panacisoli sp. nov. is proposed. The type strain is strain CJ32(T) ( = KACC 17503(T) = JCM 19226(T)).
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Affiliation(s)
- Jung-Hye Choi
- Department of Systems Biotechnology, Chung-Ang University, Anseong 456-756, Republic of Korea
| | - Chang-Jun Cha
- Department of Systems Biotechnology, Chung-Ang University, Anseong 456-756, Republic of Korea
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Abstract
A novel beige-pigmented, Gram-staining-negative, coccoid, motile and facultatively anaerobic bacteria, designated strain CJ24T, was isolated from the tidal flat sediment of the Yellow Sea in South Korea. Characterization of this strain was performed on the basis of polyphasic taxonomic methods. Phylogenetic analysis of the 16S rRNA and gyrB genes revealed that strain CJ24T belongs to the genus
Ferrimonas
, sharing the highest 16S rRNA gene sequence similarity of 96.9 % with
Ferrimonas marina
DSM 16917T. Strain CJ24T was able to grow optimally at 30 °C, at pH 6.0 and in the presence of 2 % NaCl (w/v). As an isoprenoid quinone, menaquinone (MK-7) was predominantly identified from this strain, while ubiquinone (Q-7) was also present as a minor component. The DNA G+C content of strain CJ24T was 60.2 mol%. The most abundant cellular fatty acids were C15 : 0 iso, C18 : 1ω9c, C16 : 0 and C17 : 0 iso. Therefore, strain CJ24T represents a novel species in the genus
Ferrimonas
for which the name Ferrimonas gelatinilytica sp. nov. is proposed; the type strain is CJ24T ( = KACC 17065T = JCM 18720T).
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Affiliation(s)
- Mohammad Mizanur Rahman
- Department of Systems Biotechnology, Chung-Ang University, Anseong 456-756, Republic of Korea
| | - Chang-Jun Cha
- Department of Systems Biotechnology, Chung-Ang University, Anseong 456-756, Republic of Korea
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Abstract
A novel bacterial strain designated CJ70T was isolated from tidal flat sediment in Korea. A polyphasic approach was used to identify this strain taxonomically. The isolate was Gram-stain-negative, strictly aerobic, yellow-pigmented, rod-shaped and non-motile. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain CJ70T was related most closely to
Stakelama pacifica
JLT832T with 95.7 % similarity and formed an independent phyletic line from recognized species of the genus
Sphingomonas
, comprising a clade with
Stakelama pacifica
, which is the only recognized species of the genus
Stakelama
. The predominant cellular fatty acids of strain CJ70T were C18 : 1ω7c (60.0 %), C16 : 0 (21.2 %) and C14 : 0 2-OH (5.8 %). The major isoprenoid quinone was ubiquinone-10. The G+C content of the genomic DNA was 61.4 mol%. The results obtained from this study suggested that strain CJ70T represents a novel species of the genus
Stakelama
, for which the name Stakelama sediminis sp. nov. is proposed. The type strain is CJ70T ( = KACC 16559T = JCM 18079T).
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Affiliation(s)
- Cung Nawl Thawng
- Department of Biotechnology (BK21 Program), Chung-Ang University, Anseong 456-756, Republic of Korea
| | - Sung-Joon Park
- Department of Biotechnology (BK21 Program), Chung-Ang University, Anseong 456-756, Republic of Korea
| | - Ju-Hee Cha
- Department of Biotechnology (BK21 Program), Chung-Ang University, Anseong 456-756, Republic of Korea
| | - Chang-Jun Cha
- Department of Biotechnology (BK21 Program), Chung-Ang University, Anseong 456-756, Republic of Korea
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Abstract
A Gram-stain-positive, non-motile, aerobic actinobacterium, designated strain CJ10T, was isolated from tidal flat sediment from the Yellow Sea in South Korea. Strain CJ10T grew on tryptic soy agar in the presence of 0–4 % (w/v) NaCl (optimum growth in the absence of NaCl) and at pH 6–11 (optimum pH 9). On the basis of 16S rRNA gene sequence analysis, strain CJ10T belonged to the genus
Gordonia
and showed the highest sequence similarity to
Gordonia hirsuta
DSM 44140T (97.9 %) and
Gordonia hydrophobica
DSM 44015T (97.6 %). DNA–DNA relatedness levels of strain CJ10T were 47.4 % (CJ10T as probe) and 42.2 % (
G. hirsuta
DSM 44140T as probe) to
G. hirsuta
DSM 44140T and 8.6 % (CJ10T as probe) and 9.3 % (
G. hydrophobica
DSM 44015T as probe) to
G. hydrophobica
DSM 44015T. The major isoprenoid quinone was MK-9(H2). The polar lipid profile of strain CJ10T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The predominant cellular fatty acids were C18 : 1ω9c (38.0 %), C16 : 0 (30.1 %) and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c; 17.4 %). The DNA G+C content was 67.7 mol%. Therefore, the results from our polyphasic taxonomic study suggest that strain CJ10T represents a novel species in the genus
Gordonia
, for which the name Gordonia alkaliphila sp. nov. is proposed; the type strain is CJ10T ( = KACC 16561T = JCM 18077T).
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Affiliation(s)
- Ju-Hee Cha
- Department of Biotechnology (BK21 Program), Chung-Ang University, Anseong 456-756, Republic of Korea
| | - Chang-Jun Cha
- Department of Biotechnology (BK21 Program), Chung-Ang University, Anseong 456-756, Republic of Korea
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Go H, Moore CJ, Lee M, Shin E, Jeon CO, Cha CJ, Han SH, Kim SJ, Lee SW, Lee Y, Ha NC, Kim YH, Cohen SN, Lee K. Upregulation of RNase E activity by mutation of a site that uncompetitively interferes with RNA binding. RNA Biol 2012; 8:1022-34. [PMID: 22186084 DOI: 10.4161/rna.8.6.18063] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Escherichia coli RNase E contains a site that selectively binds to RNAs containing 5'-monophosphate termini, increasing the efficiency of endonucleolytic cleavage of these RNAs. Random mutagenesis of N-Rne, the N-terminal catalytic region of RNase E, identified a hyperactive variant that remains preferentially responsive to phosphorylation at 5' termini. Biochemical analyses showed that the mutation (Q36R), which replaces glutamine with arginine at a position distant from the catalytic site, increases formation of stable RNA-protein complexes without detectably affecting the enzyme's secondary or tertiary structure. Studies of cleavage of fluorogenic substrate and EMSA experiments indicated that the Q36R mutation increases catalytic activity and RNA binding. However, UV crosslinking and mass spectrometry studies suggested that the mutant enzyme lacks an RNA binding site present in its wild-type counterpart: two substrate-bound tryptic peptides, (65) HGFLPLK (71)--which includes amino acids previously implicated in substrate binding and catalysis--and (24) LYDLDIESPGHEQK (37)--which includes the Q36 locus-were identified in wild-type enzyme complexes. Only the shorter peptide was observed for complexes containing Q36R. Our results identify a novel RNase E locus that disparately affects the number of substrate binding sites and catalytic activity of the enzyme. We propose a model that may account for these surprising effects.
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Affiliation(s)
- Hayoung Go
- School of Biological Sciences, Chung-Ang University, Seoul, Republic of Korea
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Abstract
A bacterium, designated strain CJ16(T), was isolated from the estuarine wetland of the Han River. Cells of the isolate were yellow-pigmented, Gram-stain-negative, non-motile and rod-shaped. Growth of strain CJ16(T) was observed in TSB at 5-37 °C (optimum 30 °C), at pH 5.0-9.0 (optimum pH 6.0) and with 0-3 % (w/v) NaCl (optimum 0 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CJ16(T) was most closely related to Chryseobacterium hagamense KCTC 22545(T) (97.2 % 16S rRNA gene sequence similarity). Genomic relatedness based on DNA-DNA hybridization between strain CJ16(T) and C. hagamense KCTC 22545(T) was 23 % (strain CJ16(T) as probe) and 19 % (strain KCTC 22545(T) as probe). Chemotaxonomic analysis revealed that strain CJ16(T) possessed MK-6 as the major isoprenoid quinone and sym-homospermidine as the predominant polyamine. The predominant fatty acids were iso-C15 : 0 (26.9 %), iso-C17 : 0 3-OH (16.8 %) and summed feature 9 (comprising C16 : 0 10-methyl and/or iso-C17 : 1ω9c; 10.5 %). The DNA G+C content of strain CJ16(T) was 37.9 mol%. Based on phenotypic, genotypic and phylogenetic studies, strain CJ16(T) represents a novel species of the genus Chryseobacterium, for which the name Chryseobacterium rigui sp. nov. is proposed. The type strain is CJ16(T) ( = KACC 16560(T) = JCM 18078(T)).
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Affiliation(s)
- Sung-Joon Park
- Department of Biotechnology (BK21 Program), Chung-Ang University, Anseong 456-756, Republic of Korea
| | - Jung-Hye Choi
- Department of Biotechnology (BK21 Program), Chung-Ang University, Anseong 456-756, Republic of Korea
| | - Chang-Jun Cha
- Department of Biotechnology (BK21 Program), Chung-Ang University, Anseong 456-756, Republic of Korea
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Park EJ, Chun J, Cha CJ, Park WS, Jeon CO, Bae JW. Bacterial community analysis during fermentation of ten representative kinds of kimchi with barcoded pyrosequencing. Food Microbiol 2012; 30:197-204. [DOI: 10.1016/j.fm.2011.10.011] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Revised: 10/06/2011] [Accepted: 10/07/2011] [Indexed: 12/23/2022]
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Yeo IC, Lee NK, Cha CJ, Hahm YT. Interspecies interaction of signal peptide PapR secreted by Bacillus cereus and its effect on production of antimicrobial peptide. Appl Biochem Biotechnol 2012; 166:700-10. [PMID: 22101448 DOI: 10.1007/s12010-011-9459-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Accepted: 10/24/2011] [Indexed: 12/11/2022]
Abstract
This study was carried out to investigate the interspecies interaction of PapR peptide secreted by Bacillus cereus on production of BSAP-254, an antimicrobial peptide produced by Bacillus subtilis SC-8 isolated from the Korean fermented soybean paste and exhibited narrow antagonistic activity against the B. cereus group, but not against other foodborne pathogens. PapR is a signal peptide that activates PlcR, which is a pleiotropic regulator controlling the expression of various virulence factors in B. cereus. When B. subtilis SC-8 was co-cultured with B. cereus, it completely inhibited the growth of B. cereus within 12 h, and the rate of BSAP-254 production was increased 34.2% at 12 h. Furthermore, 5 μM of synthetic PapR peptide added to the culture of B. subtilis SC-8 increased the rate of BSAP-254 production up to 59.7%. The growth of B. subtilis SC-8, however, was not significantly different with or without the addition of PapR. When B. cereus papR mutant was co-cultured with B. subtilis SC-8, the growth of the mutant was not inhibited and the rate of BSAP-254 production was decreased by 45%.
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Affiliation(s)
- In-Cheol Yeo
- Department of Biotechnology (BK21 Program), Chung-Ang University, Anseong 456-756, Republic of Korea
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Kim HJ, Eom SJ, Park SJ, Cha CJ, Kim GB. Lactobacillus alvi sp. nov., isolated from the intestinal tract of chicken. FEMS Microbiol Lett 2011; 323:83-7. [DOI: 10.1111/j.1574-6968.2011.02361.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Revised: 07/07/2011] [Accepted: 07/07/2011] [Indexed: 11/30/2022] Open
Affiliation(s)
- Hee-Jin Kim
- Department of Animal Science and Technology; Chung-Ang University; Anseong; Korea
| | - Seok-Jin Eom
- Department of Animal Science and Technology; Chung-Ang University; Anseong; Korea
| | - Sung-Joon Park
- Department of Biotechnology (BK21 Program); Chung-Ang University; Anseong; Korea
| | - Chang-Jun Cha
- Department of Biotechnology (BK21 Program); Chung-Ang University; Anseong; Korea
| | - Geun-Bae Kim
- Department of Animal Science and Technology; Chung-Ang University; Anseong; Korea
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Go H, Moore CJ, Lee M, Shin E, Jeon CO, Cha CJ, Han SH, Kim SJ, Lee SW, Lee Y, Ha NC, Kim YH, Cohen SN, Lee K. Upregulation of RNase E activity by mutation of a site that uncompetitively interferes with RNA binding. RNA Biol 2011. [PMID: 22186084 PMCID: PMC3360077 DOI: 10.4161/rna.8.6.18036] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Escherichia coli RNase E contains a site that selectively binds to RNAs containing 5'-monophosphate termini, increasing the efficiency of endonucleolytic cleavage of these RNAs. Random mutagenesis of N-Rne, the N-terminal catalytic region of RNase E, identified a hyperactive variant that remains preferentially responsive to phosphorylation at 5' termini. Biochemical analyses showed that the mutation (Q36R), which replaces glutamine with arginine at a position distant from the catalytic site, increases formation of stable RNA-protein complexes without detectably affecting the enzyme's secondary or tertiary structure. Studies of cleavage of fluorogenic substrate and EMSA experiments indicated that the Q36R mutation increases catalytic activity and RNA binding. However, UV crosslinking and mass spectrometry studies suggested that the mutant enzyme lacks an RNA binding site present in its wild-type counterpart: two substrate-bound tryptic peptides, (65) HGFLPLK (71)--which includes amino acids previously implicated in substrate binding and catalysis--and (24) LYDLDIESPGHEQK (37)--which includes the Q36 locus-were identified in wild-type enzyme complexes. Only the shorter peptide was observed for complexes containing Q36R. Our results identify a novel RNase E locus that disparately affects the number of substrate binding sites and catalytic activity of the enzyme. We propose a model that may account for these surprising effects.
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Affiliation(s)
- Hayoung Go
- School of Biological Sciences; Chung-Ang University; Seoul, Republic of Korea,Department of Genetics; Stanford University; Stanford, CA USA
| | | | - Minho Lee
- School of Biological Sciences; Chung-Ang University; Seoul, Republic of Korea
| | - Eunkyoung Shin
- School of Biological Sciences; Chung-Ang University; Seoul, Republic of Korea
| | - Che Ok Jeon
- School of Biological Sciences; Chung-Ang University; Seoul, Republic of Korea
| | - Chang-Jun Cha
- School of Biological Sciences; Chung-Ang University; Seoul, Republic of Korea
| | - Seung Hyun Han
- Department of Oral Microbiology and Immunology; Seoul National University; Seoul, Republic of Korea
| | - Su-Jin Kim
- Department of Chemistry; Korea University; Seoul, Republic of Korea
| | - Sang-Won Lee
- Department of Chemistry; Korea University; Seoul, Republic of Korea
| | - Younghoon Lee
- Department of Chemistry; KAIST; Daejeon, Republic of Korea
| | - Nam-Chul Ha
- Department of Manufacturing Pharmacy; Pusan National University; Busan, Republic of Korea
| | - Yong-Hak Kim
- Department of Microbiology; Catholic University of Daegu; Daegu, Republic of Korea
| | - Stanley N Cohen
- Department of Genetics; Stanford University; Stanford, CA USA,Department of Medicine; Stanford University; Stanford, CA USA
| | - Kangseok Lee
- School of Biological Sciences; Chung-Ang University; Seoul, Republic of Korea
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Kim KY, Park SJ, Hahm YT, Cha CJ. Marinitalea sucinacia gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from tidal flat sediment. FEMS Microbiol Lett 2010; 314:89-94. [DOI: 10.1111/j.1574-6968.2010.02147.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Abstract
Decursin and its structural isomer decursinol angelate are major secondary metabolites in the root of Angelica gigas Nakai which possess several chemotherapeutic properties. We isolated bacteria capable of transforming decursin and determined metabolites and biotransformation kinetics. Decursinol angelate was not metabolized to any significant extent. Resting cells of Mycobacterium sp. PYR1001 were able to transform decursin. After 24 h incubation, 5 mM of decursin was completely transformed to a metabolite, the structure of which was determined by NMR and mass spectral analyses to be decursinol. This conversion was shown to be catalyzed by an esterase activity, and the activity was found to be specific for decursin. These results suggest that strain PYR1001 can be successfully used to transform decursin for the production of decursinol, a compound known to have cancer chemopreventive activity.
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Affiliation(s)
- Ki-Yeon Kim
- Department of Biotechnology (BK21 Program), Chung-Ang University, Anseong 456-756, Republic of Korea
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Bae JY, Kim KY, Kim JH, Lee K, Cho JC, Cha CJ. Paenibacillus aestuarii sp. nov., isolated from an estuarine wetland. Int J Syst Evol Microbiol 2010; 60:644-647. [DOI: 10.1099/ijs.0.011544-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterial strain designated CJ25T was isolated from the estuarine wetland of the Han river in Korea. Identification of this strain was carried out on the basis of polyphasic taxonomy. The isolate was Gram-staining-positive, rod-shaped, non-pigmented and motile. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the isolate was closely related to Paenibacillus chondroitinus DSM 5051T with 96.1 % similarity. The predominant fatty acids were anteiso-C15 : 0 (50.25 %), iso-C16 : 0 (18.54 %) and iso-C15 : 0 (10.00 %). The major isoprenoid quinone was MK-7. The G+C content of genomic DNA was 50 mol%. According to physiological data and 16S rRNA gene sequence analysis, the isolate was discriminated from related members of the genus Paenibacillus. Therefore, strain CJ25T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus aestuarii sp. nov. is proposed. The type strain is CJ25T (=KACC 13125T =JCM 15521T).
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Affiliation(s)
- Jee-Yeon Bae
- Department of Biotechnology, Chung-Ang University, Anseong 456-756, Republic of Korea
| | - Ki-Yeon Kim
- Department of Biotechnology, Chung-Ang University, Anseong 456-756, Republic of Korea
| | - Ju-Hyoung Kim
- Department of Biotechnology, Chung-Ang University, Anseong 456-756, Republic of Korea
| | - Kangseok Lee
- Department of Life Science, Chung-Ang University, Seoul 156-756, Republic of Korea
| | - Jang-Cheon Cho
- Department of Biology and Ocean Sciences, Inha University, Incheon 402-751, Republic of Korea
| | - Chang-Jun Cha
- Department of Biotechnology, Chung-Ang University, Anseong 456-756, Republic of Korea
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Sim SH, Yeom JH, Shin C, Song WS, Shin E, Kim HM, Cha CJ, Han SH, Ha NC, Kim SW, Hahn Y, Bae J, Lee K. Escherichia coli ribonuclease III activity is downregulated by osmotic stress: consequences for the degradation of bdm mRNA in biofilm formation. Mol Microbiol 2009; 75:413-25. [PMID: 19943899 DOI: 10.1111/j.1365-2958.2009.06986.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
During the course of experiments aimed at identifying genes with ribonuclease III (RNase III)-dependent expression in Escherichia coli, we found that steady state levels of bdm mRNA were dependent on cellular concentrations of RNase III. The half-lives of adventitiously overexpressed bdm mRNA and the activities of a transcriptional bdm'-'cat fusion were observed to be dependent on cellular concentrations of RNase III, indicating the existence of cis-acting elements in bdm mRNA responsive to RNase III. In vitro and in vivo cleavage analyses of bdm mRNA identified two RNase III cleavage motifs, one in the 5'-untranslated region and the other in the coding region of bdm mRNA, and indicated that RNase III cleavages in the coding region constitute a rate-determining step for bdm mRNA degradation. We also discovered that downregulation of the ribonucleolytic activity of RNase III is required for the sustained elevation of RcsB-induced bdm mRNA levels during osmotic stress and that cells overexpressing bdm form biofilms more efficiently. These findings indicate that the Rcs signalling system has an additional regulatory pathway that functions to modulate bdm expression and consequently, adapt E. coli cells to osmotic stress.
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Affiliation(s)
- Se-Hoon Sim
- Department of Life Science (BK21 program), Chung-Ang University, Seoul, Republic of Korea
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