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Guo SZ, Wu T, Zhu HZ, Yan L, Liu ZP, Li DF, Jiang CY, Liu SJ, Shen XH. Niabella beijingensis sp. nov. and Thermomonas beijingensis sp. nov., two bacteria from constructed wetland. Int J Syst Evol Microbiol 2022; 72. [PMID: 35316171 PMCID: PMC9558575 DOI: 10.1099/ijsem.0.005280] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Two Gram-stain-negative, aerobic, non-motile and rod-shaped bacterial strains designated 3A5MI-3T and RSS-23T were isolated from the Dragon-shaped Wetland System in Beijing Olympic Park, PR China. Strain 3A5MI-3T grew at 15–45 °C, pH 5.0–9.0 and with 0–2 % NaCl (w/v), and strain RSS-23T grew at 15-40 oC, pH 5.5–9.0 and with 0–1 % NaCl (w/v). Phylogenetic analyses of 16S rRNA gene sequences revealed that strains 3A5MI-3T and RSS-23T were members of Bacteroidetes and Proteobacteria, respectively. Phylogenetically closest relatives of strains 3A5MI-3T and RSS-23T were Niabella pedocola R384T and Thermomonas aquatica SY21T, respectively. The cells of strain 3A5MI-3T contained menaquinone MK-7 and phosphatidylethanolamine, and the major cellular fatty acids were composed of iso-C15 : 0, iso-C15 : 1 ω6c and/or iso-C15 : 1 ω7c, iso-C17 : 0 3-OH, C16 : 0 and summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c). Strain RSS-23T contained ubiquinone Q-8 and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unknown phospholipids and an unknown lipid, and its major cellular fatty acids were iso-C15 : 0, iso-C17 : 1 ω9c, iso-C11 : 0 3-OH and summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c). DNA sequencing resulted in 6.59 Mb for the strain 3A5MI-3T genome and 2.79 Mb for the strain RSS-23T genome. The calculated G+C molar contents for strains 3A5MI-3T and RSS-23T were 47.07 and 61.21 mol%, respectively. According to phenotypic and phylogenetic characteristics, strains 3A5MI-3T and RSS-23T represent novel species of the genera Niabella and Thermomonas for which the names Niabella beijingensis sp. nov. and Thermomonas beijingensis sp. nov. are proposed. The type strain for N. beijingensis sp. nov. is 3A5MI-3T (=CGMCC 1.17737T=KCTC 82817T). The type strain for T. beijingensis sp. nov. is RSS-23T (=CGMCC 1.17738T=KCTC 82820T).
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Affiliation(s)
- Sheng-Zhi Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Tong Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Hai-Zhen Zhu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Lei Yan
- University of Chinese Academy of Sciences, Beijing 100049, PR China
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Zhi-Pei Liu
- University of Chinese Academy of Sciences, Beijing 100049, PR China
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - De-Feng Li
- University of Chinese Academy of Sciences, Beijing 100049, PR China
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Cheng-Ying Jiang
- University of Chinese Academy of Sciences, Beijing 100049, PR China
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao 266237, PR China
| | - Xi-Hui Shen
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
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Kang M, Yang J, Kim S, Park J, Kim M, Park W. Occurrence of antibiotic resistance genes and multidrug-resistant bacteria during wastewater treatment processes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 811:152331. [PMID: 34915016 DOI: 10.1016/j.scitotenv.2021.152331] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/11/2021] [Accepted: 12/07/2021] [Indexed: 05/09/2023]
Abstract
Wastewater treatment plants (WWTPs) constantly receive a wide variety of contaminants, including pharmaceuticals, and are potential reservoirs of antibiotic resistance genes (ARGs). This favors the development of multidrug-resistant bacteria (MRB) through horizontal gene transfer. Samples from five different WWTP processes were collected in September 2020 and January 2021 to monitor ARG resistomes and culturable MRB in the presence of eight different antibiotics. Nanopore-based ARG abundance and bacterial community analyses suggested that ARG accumulation favors the generation of MRB. Activated and mixed sludges tended to have lower bacterial diversity and ARG abundance because of selective forces that favored the growth of specific microorganisms during aeration processes. Escherichia strains enriched in WWTPs (up to 71%) were dominant in all the samples, whereas Cloacamonas species were highly abundant only in anaerobically digested sludge samples (60%-79%). Two ARG types [sulfonamide resistance genes (sul1) and aminoglycoside resistance genes (aadA1, aadA13, and aadA2)] were prevalent in all the processes. The total counts of culturable MRB, such as Niabella, Enterococcus, Bacillus, and Chryseobacterium species, gradually increased during aerobic WWTP processes. Genomic analyses of all MRB isolated from the samples revealed that the resistome of Enterococcus species harbored the highest number of ARGs (7-18 ARGs), commonly encoding ant(6)-la, lnu(B), erm(B), and tet(S/M). On the other hand, Niablella strains possibly had intrinsic resistant phenotypes without ARGs. All MRB possessed ARGs originating from the same mobile genetic elements, suggesting that WWTPs are hotspots for the migration of ARGs and emergence of MRB.
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Affiliation(s)
- Mingyeong Kang
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Jihye Yang
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Suhyun Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Jaeeun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Misung Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea.
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Siddiqi MZ, Huq MA, Im WT. Isolation, characterisation and genome analysis of a novel ginsenosides hydrolysing bacterium Ginsengibacter hankyongi gen. nov., sp. nov. isolated from soil. Antonie van Leeuwenhoek 2020; 114:11-22. [PMID: 33226510 DOI: 10.1007/s10482-020-01485-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 10/16/2020] [Indexed: 11/25/2022]
Abstract
A novel yellow-pigmented bacterial strain (designated BR5-29T), was isolated and its taxonomy was studied. Phylogenetic study based on the 16S rRNA and draft genome sequence placed the strain BR5-29T in a distinct lineage within the family Chitinophagaceae, sharing ≤ 93.4% sequence similarity with members of the closely related genera Ferruginibacter, Flavisolibacter, Flavitalea and Niastella. The novel isolate showed the highest sequence similarity to the genus Ferruginibacter. The draft genome of strain BR5-29T had a total length of 5,505,520 base pairs. A total of 4585 genes were identified, in which 4537 were CDS and 48 RNA genes were assigned a putative function. The genome annotation of BR5-29T showed 225 carbohydrate genes which may be responsible for the conversion of major ginsenosides to minor ginsenosides. Strain BR5-29T contained MK-7 as a predominant quinone, and iso-C15:0, iso-C15:0 G, iso-C17:0 3-OH, and C16:1 ω7c and/or C16:1 ω6c (summed feature 3) as major fatty acids. The polar lipids found in the strain BR5-29T were phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), five unidentified polar lipids (L1-L5), two unidentified aminolipid and one unidentified aminophospholipid. Our pilot data demonstrate that the novel isolate shares the similar major polar lipid PE, major quinone MK-7 and major fatty acids with the described members of the family Chitinophagaceae. However, the low 16S rRNA gene sequence (< 93.4%), the little high amount of C12:0, iso-C17:0 2-OH and iso-C15:1 2-OH fatty acids, low DNA G + C content, and the presence of DPG, PG and two unidentified polar lipids (L1 and L3 differentiate the BR5-29T from its closest phylogenetic neighbors. Thus, the isolate represents a novel genus and species in the family Chitinophagaceae for which the name Ginsengibacter hankyongi gen. nov., sp. nov. is proposed. The type strain is BR5-29T (= KACC 19446T = LMG 30462T). Thus, we predict that this novel strain may prove useful for the future research analysis (target gene cloning) and mass production of Rg3.
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Affiliation(s)
- Muhammad Zubair Siddiqi
- Department of Biotechnology, Hankyong National University, 327 Chungang-no, Anseong-si, Kyonggi-do, 17579, Republic of Korea.,AceEMzyme Co., Ltd, Academic Industry Cooperation, 327 Chungang-no, Anseong-si, Kyonggi-do, 17579, Republic of Korea
| | - Md Amdadul Huq
- Department of Food and Nutrition, College of Biotechnology and Natural Resource, Chung-Ang University, Gyeonggi-do, Anseong-si, 17546, Republic of Korea
| | - Wan-Taek Im
- Department of Biotechnology, Hankyong National University, 327 Chungang-no, Anseong-si, Kyonggi-do, 17579, Republic of Korea. .,AceEMzyme Co., Ltd, Academic Industry Cooperation, 327 Chungang-no, Anseong-si, Kyonggi-do, 17579, Republic of Korea.
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Abarca JG, Zuniga I, Ortiz-Morales G, Lugo A, Viquez-Cervilla M, Rodriguez-Hernandez N, Vázquez-Sánchez F, Murillo-Cruz C, Torres-Rivera EA, Pinto-Tomás AA, Godoy-Vitorino F. Characterization of the Skin Microbiota of the Cane Toad Rhinella cf. marina in Puerto Rico and Costa Rica. Front Microbiol 2018; 8:2624. [PMID: 29354109 PMCID: PMC5760547 DOI: 10.3389/fmicb.2017.02624] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 12/15/2017] [Indexed: 12/22/2022] Open
Abstract
Rhinella marina is a toad native to South America that has been introduced in the Antilles, likely carrying high loads of microorganisms, potentially impacting local community diversity. The amphibian skin is involved in pathogen defense and its microbiota has been relatively well studied, however, research focusing on the cane toad microbiota is lacking. We hypothesize that the skin microbial communities will differ between toads inhabiting different geographical regions in Central America and the Caribbean. To test our hypothesis, we compared the microbiota of three populations of R. cf. marina toads, two from Costa Rican (native) and one Puerto Rican (exotic) locations. In Costa Rica, we collected 11 toads, 7 in Sarapiquí and 4 from Turrialba while in Puerto Rico, 10 animals were collected in Santa Ana. Separate swab samples were collected from the dorsal and ventral sites resulting in 42 samples. We found significant differences in the structure of the microbial communities between Puerto Rico and Costa Rica. We detected as much as 35 different phyla; however, communities were dominated by Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. Alpha diversity and richness were significantly higher in toads from Puerto Rico and betadiversity revealed significant differences between the microbiota samples from the two countries. At the genus level, we found in Santa Ana, Puerto Rico, a high dominance of Kokuria, Niabella, and Rhodobacteraceae, while in Costa Rica we found Halomonas and Pseudomonas in Sarapiquí, and Acinetobacter and Citrobacter in Turrialba. This is the first report of Niabella associated with the amphibian skin. The core microbiome represented 128 Operational Taxonomic Units (OTUs) mainly from five genera shared among all samples, which may represent the symbiotic Rhinella's skin. These results provide insights into the habitat-induced microbial changes facing this amphibian species. The differences in the microbial diversity in Puerto Rican toads compared to those in Costa Rica provide additional evidence of the geographically induced patterns in the amphibian skin microbiome, and highlight the importance of discussing the microbial tradeoffs in the colonization of new ecosystems.
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Affiliation(s)
- Juan G. Abarca
- Centro de Investigación en Estructuras Microscópicas, Universidad de Costa Rica, San Pedro de Montes de Oca, Costa Rica
| | - Ibrahim Zuniga
- Centro de Investigación en Estructuras Microscópicas, Universidad de Costa Rica, San Pedro de Montes de Oca, Costa Rica
- Departamento de Bioquímica, Escuela de Medicina, Universidad de Costa Rica, San Pedro de Montes de Oca, Costa Rica
- Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, San Pedro de Montes de Oca, Costa Rica
| | - Gilmary Ortiz-Morales
- Department of Natural Sciences, Microbial Ecology and Genomics Laboratory, Inter American University of Puerto Rico, Metropolitan Campus, San Juan, Puerto Rico
| | - Armando Lugo
- Department of Natural Sciences, Microbial Ecology and Genomics Laboratory, Inter American University of Puerto Rico, Metropolitan Campus, San Juan, Puerto Rico
| | - Mariel Viquez-Cervilla
- Centro de Investigación en Estructuras Microscópicas, Universidad de Costa Rica, San Pedro de Montes de Oca, Costa Rica
| | - Natalia Rodriguez-Hernandez
- Centro de Investigación en Estructuras Microscópicas, Universidad de Costa Rica, San Pedro de Montes de Oca, Costa Rica
| | - Frances Vázquez-Sánchez
- Department of Natural Sciences, Microbial Ecology and Genomics Laboratory, Inter American University of Puerto Rico, Metropolitan Campus, San Juan, Puerto Rico
| | - Catalina Murillo-Cruz
- Centro de Investigación en Estructuras Microscópicas, Universidad de Costa Rica, San Pedro de Montes de Oca, Costa Rica
| | - Ernesto A. Torres-Rivera
- Department of Natural Sciences, Center for Environmental Education, Conservation and Interpretation, Inter American University of Puerto Rico, Metropolitan Campus, San Juan, Puerto Rico
| | - Adrián A. Pinto-Tomás
- Centro de Investigación en Estructuras Microscópicas, Universidad de Costa Rica, San Pedro de Montes de Oca, Costa Rica
- Departamento de Bioquímica, Escuela de Medicina, Universidad de Costa Rica, San Pedro de Montes de Oca, Costa Rica
- Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, San Pedro de Montes de Oca, Costa Rica
| | - Filipa Godoy-Vitorino
- Department of Natural Sciences, Microbial Ecology and Genomics Laboratory, Inter American University of Puerto Rico, Metropolitan Campus, San Juan, Puerto Rico
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Medeiros JD, Leite LR, Pylro VS, Oliveira FS, Almeida VM, Fernandes GR, Salim ACM, Araújo FMG, Volpini AC, Oliveira G, Cuadros-Orellana S. Single-cell sequencing unveils the lifestyle and CRISPR-based population history of Hydrotalea
sp. in acid mine drainage. Mol Ecol 2017; 26:5541-5551. [DOI: 10.1111/mec.14294] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 07/21/2017] [Accepted: 07/27/2017] [Indexed: 01/20/2023]
Affiliation(s)
- J. D. Medeiros
- Biosystems Informatics and Genomics Group; René Rachou Research Center; FIOCRUZ-MG; Belo Horizonte MG Brazil
- Institute of Biological Sciences; Federal University of Minas Gerais; UFMG; Belo Horizonte MG Brazil
| | - L. R. Leite
- Biosystems Informatics and Genomics Group; René Rachou Research Center; FIOCRUZ-MG; Belo Horizonte MG Brazil
- Institute of Biological Sciences; Federal University of Minas Gerais; UFMG; Belo Horizonte MG Brazil
| | - V. S. Pylro
- Biosystems Informatics and Genomics Group; René Rachou Research Center; FIOCRUZ-MG; Belo Horizonte MG Brazil
- Department of Soil Science; “Luiz de Queiroz” College of Agriculture; University of São Paulo; ESALQ/USP; Piracicaba SP Brazil
| | - F. S. Oliveira
- Biosystems Informatics and Genomics Group; René Rachou Research Center; FIOCRUZ-MG; Belo Horizonte MG Brazil
- Institute of Biological Sciences; Federal University of Minas Gerais; UFMG; Belo Horizonte MG Brazil
| | - V. M. Almeida
- Biosystems Informatics and Genomics Group; René Rachou Research Center; FIOCRUZ-MG; Belo Horizonte MG Brazil
- Institute of Biological Sciences; Federal University of Minas Gerais; UFMG; Belo Horizonte MG Brazil
| | - G. R. Fernandes
- Biosystems Informatics and Genomics Group; René Rachou Research Center; FIOCRUZ-MG; Belo Horizonte MG Brazil
| | - A. C. M. Salim
- Biosystems Informatics and Genomics Group; René Rachou Research Center; FIOCRUZ-MG; Belo Horizonte MG Brazil
| | - F. M. G. Araújo
- Biosystems Informatics and Genomics Group; René Rachou Research Center; FIOCRUZ-MG; Belo Horizonte MG Brazil
| | - A. C. Volpini
- Biosystems Informatics and Genomics Group; René Rachou Research Center; FIOCRUZ-MG; Belo Horizonte MG Brazil
| | - G. Oliveira
- Biosystems Informatics and Genomics Group; René Rachou Research Center; FIOCRUZ-MG; Belo Horizonte MG Brazil
- Vale Institute of Technology - Sustainable Development; Belém PA Brazil
| | - S. Cuadros-Orellana
- Biosystems Informatics and Genomics Group; René Rachou Research Center; FIOCRUZ-MG; Belo Horizonte MG Brazil
- Centro de Biotecnología de los Recursos Naturales; Facultad de Ciencias Agrarias y Forestales; Universidad Católica del Maule; Talca Chile
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Siddiqi MZ, Aslam Z, Im WT. Arachidicoccus ginsenosidivorans sp. nov., with ginsenoside-converting activity isolated from ginseng cultivating soil. Int J Syst Evol Microbiol 2017; 67:1005-1010. [PMID: 27974091 DOI: 10.1099/ijsem.0.001720] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-reaction-negative, catalase- and oxidase-positive, aerobic, non-motile, light yellow and rod-shaped bacterium (designated Gsoil 809T) isolated from soil of ginseng field, was characterized by a polyphasic approach to clarify its taxonomic position. Strain Gsoil 809T was observed to grow optimally at 30 °C and at pH 7.0 on nutrient agar medium. Strain Gsoil 809T possessed β-glucosidase activity, which was responsible for its ability to transform protopanaxatriol-type ginsenoside Rg1 to ginsenoside Rh1. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain Gsoil 809T belongs to the genus Arachidicoccus of the family Chitinophagaceae and was most closely related to Arachidicoccusrhizosphaerae Vu-144T (98.1 % 16S rRNA gene sequence similarity). The DNA G+C content was 39.4 mol%. The DNA-DNA hybridization value between strain Gsoil 809T and A.rhizosphaerae Vu-144T was 41.27±1.03 %. The major polar lipids were phosphatidylethanolamine and an unknown polar lipid. The predominant quinone was MK-7. The major fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH and summed feature 3, which supported the affiliation of Gsoil 809T to the genus Arachidicoccus. Strain Gsoil 809T contained homospermidineas the major polyamine. Moreover, the physiological and biochemical test results and low DNA-DNA relatedness value allowed the phenotypic and genotypic differentiation of strain Gsoil 809T from recognized species of the genus Arachidicoccus. Therefore, strain Gsoil 809T represents a novel species of the genus Arachidicoccus, for which the name Arachidicoccus ginsenosidivorans sp. nov. is proposed. The type strain is Gsoil 809T (=KCTC 22820T=JCM 30984T).
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Affiliation(s)
- Muhammad Zubair Siddiqi
- Department of Biotechnology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea
- Center for Genetic Information, Graduate School of Bio and Information Technology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea
| | - Zubair Aslam
- Department of Agronomy, Faculty of Agriculture, University of Agriculture, Faisalabad-38040, Pakistan
| | - Wan-Taek Im
- Center for Genetic Information, Graduate School of Bio and Information Technology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea
- Department of Biotechnology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea
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Ngo HTT, Trinh H, Yan ZF, Moya G, Kook M, Yi TH. Niabella hibiscisoli sp. nov., isolated from soil of a Rose of Sharon garden. Int J Syst Evol Microbiol 2016; 67:784-788. [PMID: 27902198 DOI: 10.1099/ijsem.0.001595] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, strictly aerobic, non-motile, rod-shaped and yellow-pigmented bacterium, designated strain THG-DN5.5T, was isolated from soil of a Rose of Sharon garden in Daejeon, South Korea. According to 16S rRNA gene sequence comparisons, strain THG-DN5.5T was found to be most closely related to Niabella yanshanensis CCBAU 05354T (97.7 % sequence similarity), Niabella ginsengisoli GR10-1T (97.0 %), 'Niabella terrae' ICM 1-15 (96.0 %), Niabella soli DSM 19437T (95.7 %) and Niabella aquatica RP-2T (95.6 %). The DNA-DNA relatedness between strain THG-DN5.5T and its phylogenetically closest neighbours was below 50.0 %. The DNA G+C content was 43.1 mol%. The major polar lipid of strain THG-DN5.5T was found to be phosphatidylethanolamine. The major fatty acids were identified as C16 : 0, iso-C15 : 0, iso-C15 : 1 G, and iso-C17 : 0 3-OH. MK-7 was the only menaquinone present. These data supported the affiliation of strain THG-DN5.5T to the genus Niabella. Strain THG-DN5.5T was distinguished from related species of the genus Niabellaby physiological and biochemical tests. In conclusion, strain THG-DN5.5T represents a novel species of the genus Niabella, for which the name Niabella hibiscisolisp. nov. is proposed. The type strain is THG-DN5.5T (=KACC 18857T=CCTCC AB 2016086T).
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Affiliation(s)
- Hien T T Ngo
- College of Life Sciences, Kyung Hee University, 1732, Deogyeong-daero, Giheung-gu, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Huan Trinh
- College of Life Sciences, Kyung Hee University, 1732, Deogyeong-daero, Giheung-gu, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Zheng-Fei Yan
- College of Life Sciences, Kyung Hee University, 1732, Deogyeong-daero, Giheung-gu, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Gabriela Moya
- College of Life Sciences, Kyung Hee University, 1732, Deogyeong-daero, Giheung-gu, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - MooChang Kook
- Department of Marine Biotechnology, Anyang University, Incheon 417-833, Republic of Korea
| | - Tae-Hoo Yi
- College of Life Sciences, Kyung Hee University, 1732, Deogyeong-daero, Giheung-gu, Yongin-si, Gyeonggi-do 17104, Republic of Korea
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Siddiqi MZ, Muhammad Shafi S, Choi KD, Im WT. Panacibacter ginsenosidivorans gen. nov., sp. nov., with ginsenoside converting activity isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2016; 66:4039-4045. [DOI: 10.1099/ijsem.0.001307] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Muhammad Zubair Siddiqi
- Department of Biotechnology, Hankyoung National University, 327 Chungang-no, Anseong-si, Kyonggi-do 17579, Republic of Korea
- Center for Genetic Information, Graduate School of Bio and Information Technology, Hankyoung National University, 327 Chungang-no, Anseong-si, Kyonggi-do 17579, Republic of Korea
| | - Siddiqi Muhammad Shafi
- Chemical Research Department, Green Planet Co. Ltd, Okayama ken, tsushima nishizaka2 chome 5-41-203, Okayama, Japan
| | - Kang Duk Choi
- Department of Biotechnology, Hankyoung National University, 327 Chungang-no, Anseong-si, Kyonggi-do 17579, Republic of Korea
- Center for Genetic Information, Graduate School of Bio and Information Technology, Hankyoung National University, 327 Chungang-no, Anseong-si, Kyonggi-do 17579, Republic of Korea
| | - Wan-Taek Im
- Center for Genetic Information, Graduate School of Bio and Information Technology, Hankyoung National University, 327 Chungang-no, Anseong-si, Kyonggi-do 17579, Republic of Korea
- Department of Biotechnology, Hankyoung National University, 327 Chungang-no, Anseong-si, Kyonggi-do 17579, Republic of Korea
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Siddiqi MZ, Muhammad Shafi S, Choi KD, Im WT. Compostibacter hankyongensis gen. nov., sp. nov., isolated from compost. Int J Syst Evol Microbiol 2016; 66:3681-3687. [PMID: 27335062 DOI: 10.1099/ijsem.0.001252] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterial strain, designated strain BS27T, was isolated from mushroom compost and subjected to a taxonomic study using a polyphasic approach. Colonies of BS27T were milky-white, circular with regular fringes and opaque. Cells were short rods, 0.3-0.5 µm wide and 1.2-2.0 µm long. Phylogenetic study based on the 16S rRNA gene sequence placed BS27T in a distinct lineage in the family Chitinophagaceae, sharing 90.1-90.9 % sequence similarity with members of the closely related genera Chitinophaga, Flavitalea, Flavihumibacter, Lacibacter and Flavisolibacter. The novel isolate showed the highest sequence similarities with the members of the genus Chitinophaga. BS27T contained MK-7 as predominant quinone, and iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 1ω7c and/or C16 : 1ω6c (summed feature 3) and iso-C17 : 1I and/or anteiso-C17 : 1B (summed feature 4) as major fatty acids. The DNA G+C content was 53.0 mol%. The major polar lipids of BS27T were phosphatidylethanolamine (PE) and five unidentified polar lipids (L1, L2, L5, L6 and L7). The results of physiological and biochemical tests allowed phenotypic differentiation of BS27T from its closest phylogenetic neighbours. On the basis of the evidence of this polyphasic study, isolate BS27T represents a novel genus and species in the family Chitinophagaceae for which the name Compostibacter hankyongensisgen. nov., sp. nov. is proposed. The type strain is BS27T (=KACC 18745T=JCM 17664T).
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Affiliation(s)
- Muhammad Zubair Siddiqi
- Department of Biotechnology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea.,Center for Genetic Information, Graduate School of Bio and Information Technology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea
| | | | - Kang Duk Choi
- Department of Biotechnology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea.,Center for Genetic Information, Graduate School of Bio and Information Technology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea
| | - Wan-Taek Im
- Center for Genetic Information, Graduate School of Bio and Information Technology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea.,Department of Biotechnology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 456-749, Republic of Korea
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