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Jo H, Park MS, Lim Y, Kang I, Cho JC. Ten Novel Species Belonging to the Genus Flavobacterium, Isolated from Freshwater Environments: F. praedii sp. nov., F. marginilacus sp. nov., F. aestivum sp. nov., F. flavigenum sp. nov., F. luteolum sp. nov., F. gelatinilyticum sp. nov., F. aquiphilum sp. nov., F. limnophilum sp. nov., F. lacustre sp. nov., and F. eburneipallidum sp. nov. J Microbiol 2023:10.1007/s12275-023-00054-4. [PMID: 37219690 DOI: 10.1007/s12275-023-00054-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 05/24/2023]
Abstract
Eleven bacterial strains were isolated from freshwater environments and identified as Flavobacterium based on 16S rRNA gene sequence analyses. Complete genome sequences of the 11 strains ranged from 3.45 to 5.83 Mb with G + C contents of 33.41-37.31%. The average nucleotide identity (ANI) values showed that strains IMCC34515T and IMCC34518 belonged to the same species, while the other nine strains represented each separate species. The ANI values between the strains and their closest Flavobacterium species exhibited ≤ 91.76%, indicating they represent each novel species. All strains had similar characteristics such as being Gram-stain-negative, rod-shaped, and contained iso-C15:0 as the predominant fatty acid, menaquinone-6 as the respiratory quinone, and phosphatidylethanolamine and aminolipids as major polar lipids. Genomic, phylogenetic, and phenotypic characterization confirmed that the 11 strains were distinct from previously recognized Flavobacterium species. Therefore, Flavobacterium praedii sp. nov. (IMCC34515T = KACC 22282 T = NBRC 114937 T), Flavobacterium marginilacus sp. nov. (IMCC34673T = KACC 22284 T = NBRC 114940 T), Flavobacterium aestivum sp. nov. (IMCC34774T = KACC 22285 T = NBRC 114941 T), Flavobacterium flavigenum sp. nov. (IMCC34775T = KACC 22286 T = NBRC 114942 T), Flavobacterium luteolum sp. nov. (IMCC34776T = KACC 22287 T = NBRC 114943 T), Flavobacterium gelatinilyticum sp. nov. (IMCC34777T = KACC 22288 T = NBRC 114944 T), Flavobacterium aquiphilum sp. nov. (IMCC34779T = KACC 22289 T = NBRC 114945 T), Flavobacterium limnophilum sp. nov. (IMCC36791T = KACC 22290 T = NBRC 114947 T), Flavobacterium lacustre sp. nov. (IMCC36792T = KACC 22291 T = NBRC 114948 T), and Flavobacterium eburneipallidum sp. nov. (IMCC36793T = KACC 22292 T = NBRC 114949 T) are proposed as novel species.
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Affiliation(s)
- Hyunyoung Jo
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea
| | - Miri S Park
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea
| | - Yeonjung Lim
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea
| | - Ilnam Kang
- Center for Molecular and Cell Biology, Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea
| | - Jang-Cheon Cho
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea.
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Kim J, Cha IT, Lee KE, Son YK, Yu J, Seol D. Characteristics and adaptability of Flavobacterium panici BSSL-CR3 in tidal flat revealed by comparative genomic and enzymatic analysis. Arch Microbiol 2022; 205:22. [PMID: 36495352 DOI: 10.1007/s00203-022-03359-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 11/22/2022] [Accepted: 11/29/2022] [Indexed: 12/13/2022]
Abstract
Tidal flat microbes play an important ecological role by removing organic pollutants and providing an energy source. However, bacteria isolated from tidal flats and their genomes have been scarcely reported, making it difficult to elucidate which genes and pathways are potentially involved in the above roles. In this study, strain BSSL-CR3, the third reported species among the tidal flat Flavobacterium was analyzed using whole-genome sequencing to investigate its adaptability and functionality in tidal flats. BSSL-CR3 is comprised of a circular chromosome of 5,972,859 bp with a GC content of 33.84%. Genome annotation and API ZYM results showed that BSSL-CR3 has a variety of secondary metabolic gene clusters and enzyme activities including α-galactosidase. BSSL-CR3 had more proteins with a low isoelectric point (pI) than terrestrial Flavobacterium strains, and several genes related to osmotic regulation were found in the genomic island (GI). Comparative genomic analysis with other tidal flat bacteria also revealed that BSSL-CR3 had the largest number of genes encoding Carbohydrate Active EnZymes (CAZymes) which are related to algae degradation. This study will provide insight into the adaptability of BSSL-CR3 to the tidal flats and contribute to facilitating future comparative analysis of bacteria in tidal flats.
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Affiliation(s)
- Jina Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul, 08826, Republic of Korea
| | - In-Tae Cha
- Microorganism Resources Division, National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon, 22689, Republic of Korea
| | - Ki-Eun Lee
- Microorganism Resources Division, National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon, 22689, Republic of Korea
| | - Youn Kyoung Son
- Microorganism Resources Division, National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon, 22689, Republic of Korea
| | - Jaewoong Yu
- eGnome, Inc., 26 Beobwon-ro 9-gil, Songpa-gu, Seoul, 05836, Republic of Korea.
| | - Donghyeok Seol
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul, 08826, Republic of Korea.
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Králová S, Busse HJ, Bezdíček M, Sandoval-Powers M, Nykrýnová M, Staňková E, Krsek D, Sedláček I. Flavobacterium flabelliforme sp. nov. and Flavobacterium geliluteum sp. nov., Two Multidrug-Resistant Psychrotrophic Species Isolated From Antarctica. Front Microbiol 2021; 12:729977. [PMID: 34745033 PMCID: PMC8570120 DOI: 10.3389/fmicb.2021.729977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 09/27/2021] [Indexed: 11/13/2022] Open
Abstract
Despite unfavorable Antarctic conditions, such as cold temperatures, freeze-thaw cycles, high ultraviolet radiation, dryness and lack of nutrients, microorganisms were able to adapt and surprisingly thrive in this environment. In this study, eight cold-adapted Flavobacterium strains isolated from a remote Antarctic island, James Ross Island, were studied using a polyphasic taxonomic approach to determine their taxonomic position. Phylogenetic analyses based on the 16S rRNA gene and 92 core genes clearly showed that these strains formed two distinct phylogenetic clusters comprising three and five strains, with average nucleotide identities significantly below 90% between both proposed species as well as between their closest phylogenetic relatives. Phenotyping revealed a unique pattern of biochemical and physiological characteristics enabling differentiation from the closest phylogenetically related Flavobacterium spp. Chemotaxonomic analyses showed that type strains P4023T and P7388T were characterized by the major polyamine sym-homospermidine and a quinone system containing predominantly menaquinone MK-6. In the polar lipid profile phosphatidylethanolamine, an ornithine lipid and two unidentified lipids lacking a functional group were detected as major lipids. These characteristics along with fatty acid profiles confirmed that these species belong to the genus Flavobacterium. Thorough genomic analysis revealed the presence of numerous cold-inducible or cold-adaptation associated genes, such as cold-shock proteins, proteorhodopsin, carotenoid biosynthetic genes or oxidative-stress response genes. Genomes of type strains surprisingly harbored multiple prophages, with many of them predicted to be active. Genome-mining identified biosynthetic gene clusters in type strain genomes with a majority not matching any known clusters which supports further exploratory research possibilities involving these psychrotrophic bacteria. Antibiotic susceptibility testing revealed a pattern of multidrug-resistant phenotypes that were correlated with in silico antibiotic resistance prediction. Interestingly, while typical resistance finder tools failed to detect genes responsible for antibiotic resistance, genomic prediction confirmed a multidrug-resistant profile and suggested even broader resistance than tested. Results of this study confirmed and thoroughly characterized two novel psychrotrophic Flavobacterium species, for which the names Flavobacterium flabelliforme sp. nov. and Flavobacterium geliluteum sp. nov. are proposed.
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Affiliation(s)
- Stanislava Králová
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Brno, Czechia
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität Wien, Vienna, Austria
| | - Matěj Bezdíček
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno, Brno, Czechia.,Department of Internal Medicine - Hematology and Oncology, Masaryk University, Brno, Czechia
| | | | - Markéta Nykrýnová
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia
| | - Eva Staňková
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Brno, Czechia
| | - Daniel Krsek
- NRL for Diagnostic Electron Microscopy of Infectious Agents, National Institute of Public Health, Prague, Czechia
| | - Ivo Sedláček
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Brno, Czechia
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