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Radzlin N, Yaakop AS, Goh KM, Liew KJ, Zakaria II, Kahar UM. Genome Analysis of Celeribacter sp. PS-C1 Isolated from Sekinchan Beach in Selangor, Malaysia, Reveals Its β-Glucosidase and Licheninase Activities. Microorganisms 2022; 10:microorganisms10020410. [PMID: 35208867 PMCID: PMC8874975 DOI: 10.3390/microorganisms10020410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/06/2022] [Accepted: 02/08/2022] [Indexed: 11/16/2022] Open
Abstract
A halophilic marine bacterial strain, PS-C1, was isolated from Sekinchan beach in Selangor, Malaysia. The 16S rRNA gene sequence analysis indicated that strain PS-C1 was associated with the genus Celeribacter. To date, there have been no reports on enzymes from the genus Celeribacter. The present study reports on the cellular features of Celeribacter sp. PS-C1, its annotated genome sequence, and comparative genome analyses of Celeribacter glycoside hydrolase (GH) enzymes. The genome of strain PS-C1 has a size of 3.87 Mbp and a G+C content of 59.10%, and contains 3739 protein-coding genes. Detailed analysis using the Carbohydrate-Active enZYmes (CAZy) database revealed that Celeribacter genomes harboured at least 12 putative genes encoding industrially important GHs that are grouped as cellulases, β-glucanases, hemicellulases, and starch-degrading enzymes. Herein, the potential applications of these enzymes are discussed. Furthermore, the activities of two types of GHs (β-glucosidase and licheninase) in strain PS-C1 were demonstrated. These findings suggest that strain PS-C1 could be a reservoir of novel GH enzymes for lignocellulosic biomass degradation.
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Affiliation(s)
- Nurfatini Radzlin
- Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Jalan Bangi, Kajang 43000, Selangor, Malaysia; (N.R.); (I.I.Z.)
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Amira Suriaty Yaakop
- School of Biological Sciences, Universiti Sains Malaysia, Minden 11800, Pulau Pinang, Malaysia
- Correspondence: (A.S.Y.); (U.M.K.)
| | - Kian Mau Goh
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia; (K.M.G.); (K.J.L.)
| | - Kok Jun Liew
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia; (K.M.G.); (K.J.L.)
| | - Iffah Izzati Zakaria
- Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Jalan Bangi, Kajang 43000, Selangor, Malaysia; (N.R.); (I.I.Z.)
| | - Ummirul Mukminin Kahar
- Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Jalan Bangi, Kajang 43000, Selangor, Malaysia; (N.R.); (I.I.Z.)
- Correspondence: (A.S.Y.); (U.M.K.)
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2
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Li Y, Ding YY, Dang YR, Bai Y, Guan L, Liu NH, Wang YZ, Kang ML, Zhang YQ, Zhang XY. Celeribacter litoreus sp. nov., isolated from intertidal sediment. Int J Syst Evol Microbiol 2022; 72. [PMID: 35156916 DOI: 10.1099/ijsem.0.005241] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, aerobic, non-flagellated and rod-shaped bacterium, strain ASW11-22T, was isolated from an intertidal sediment collected from a coastal area of Qingdao, PR China. The strain grew at 15-40 °C (optimum, 37 °C), at pH 6.0-9.0 (optimum, pH 7.0) and with 0.5-10 % (w/v) NaCl (optimum, 1.0 %). It hydrolysed gelatin and aesculin but did not reduce nitrate to nitrite. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain ASW11-22T belonged to the genus Celeribacter, showing the highest sequence similarity to the type strains of Celeribacter halophilus MCCC 1A06432T (98.20 %) and Celeribacter ethanolicus NH195T (97.84 %). The genomic DNA G+C content was 59.1 mol%. The major cellular fatty acid (>10 %) of the strain was summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and its main polar lipids were phosphatidylglycerol and one unidentified aminolipid. The sole respiratory quinone of strain ASW11-22T was ubiquinone-10. On the basis of the polyphasic evidence presented in this paper, strain ASW11-22T represents a novel Celeribacter species, for which the name Celeribacter litoreus sp. nov. is proposed. The type strain is ASW11-22T (=KCTC 82495T=MCCC 1K05584T).
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Affiliation(s)
- Yi Li
- College of Life Sciences, Shanxi Agricultural University, Taigu 030801, PR China.,State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Yun-Yun Ding
- College of Life Sciences, Shanxi Agricultural University, Taigu 030801, PR China
| | - Yan-Ru Dang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Yun Bai
- College of Life Sciences, Shanxi Agricultural University, Taigu 030801, PR China
| | - Li Guan
- College of Life Sciences, Shanxi Agricultural University, Taigu 030801, PR China
| | - Ning-Hua Liu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Yu-Zhu Wang
- College of Life Sciences, Shanxi Agricultural University, Taigu 030801, PR China
| | - Mei-Lin Kang
- College of Life Sciences, Shanxi Agricultural University, Taigu 030801, PR China
| | - Yu-Qiang Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
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3
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Zhu KL, Wang XQ, Zhang TS, Shang DD, Du ZJ. Salibaculum halophilum gen. nov., sp. nov. and Salibaculum griseiflavum sp. nov., in the family Rhodobacteraceae. Int J Syst Evol Microbiol 2021; 71. [PMID: 34170216 DOI: 10.1099/ijsem.0.004808] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-stain-negative, moderately halophilic, non-motile, rod-shaped, pale yellow, and aerobic strains, designated WDS1C4T and WDS4C29T, were isolated from a marine solar saltern in Weihai, Shandong Province, PR China. Growth of strain WDS1C4T occurred at 10-45 °C (optimum, 37 °C), with 4-16 % (w/v) NaCl (optimum, 8 %) and at pH 6.5-9.0 (optimum, pH 7.5). Growth of strain WDS4C29T occurred at 10-45 °C (optimum, 40 °C), with 2-18 % (w/v) NaCl (optimum, 6 %) and at pH 6.5-9.0 (optimum, pH 7.5). Q-10 was the sole respiratory quinone of the two strains. The major polar lipids of strains WDS1C4T and WDS4C29T were phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. The major cellular fatty acid in strains WDS1C4T and WDS4C29T was C18 : 1 ω7c, and the genomic DNA G+C contents of strains WDS1C4T and WDS4C29T were 67.6 and 63.3 mol%, respectively. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strains WDS1C4T and WDS4C29T were members of the family Rhodobacteraceae and showed 94.3 and 95.3 % similarities to their closest relative, Celeribacter indicus, respectively. The similarity between WDS1C4T and WDS4C29T was 97.3 %. Differential phenotypic and genotypic characteristics of the two isolates from recognized genera showed that the two strains should be classified as representing two novel species in a new genus for which the names Salibaculum halophilum gen. nov., sp. nov. (type species, type strain WDS1C4T=MCCC 1H00179T=KCTC 52542T) and Salibaculum griseiflavum sp. nov. (WDS4C29T=MCCC 1H00175T=KCTC 52541T) are proposed.
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Affiliation(s)
- Ke-Lei Zhu
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Xiao-Qun Wang
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Tian-Shu Zhang
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Dan-Dan Shang
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
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4
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Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Göker M. Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria. Front Microbiol 2020; 11:468. [PMID: 32373076 PMCID: PMC7179689 DOI: 10.3389/fmicb.2020.00468] [Citation(s) in RCA: 223] [Impact Index Per Article: 55.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 03/04/2020] [Indexed: 11/13/2022] Open
Abstract
The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.
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Affiliation(s)
- Anton Hördt
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Marina García López
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Jan P. Meier-Kolthoff
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Marcel Schleuning
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Lisa-Maria Weinhold
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czechia
| | - Brian J. Tindall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Sabine Gronow
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Markus Göker
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
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5
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Complete Genome Sequence of Celeribacter baekdonensis Strain LH4, a Thiosulfate-Oxidizing Alphaproteobacterial Isolate from Gulf of Mexico Continental Slope Sediments. GENOME ANNOUNCEMENTS 2018; 6:6/20/e00434-18. [PMID: 29773637 PMCID: PMC5958252 DOI: 10.1128/genomea.00434-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report here the closed genome sequences of Celeribacter baekdonensis strain LH4 and five unnamed plasmids obtained through PacBio sequencing with 99.99% consensus concordance. The genomes contained several distinctive features not found in other published Celeribacter genomes, including the potential to aerobically degrade styrene and other phenolic compounds.
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6
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Yang JA, Kang I, Moon M, Ryu UC, Kwon KK, Cho JC, Oh HM. Complete genome sequence of Celeribacter marinus IMCC12053T, the host strain of marine bacteriophage P12053L. Mar Genomics 2016; 26:5-7. [DOI: 10.1016/j.margen.2015.11.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 10/26/2015] [Accepted: 11/26/2015] [Indexed: 11/29/2022]
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7
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Taek Oh Y, Avedoza C, Lee SS, Jeong SE, Jia B, Jeon CO. Celeribacter naphthalenivorans sp. nov., a naphthalene-degrading bacterium from tidal flat sediment. Int J Syst Evol Microbiol 2015; 65:3073-3078. [DOI: 10.1099/ijs.0.000381] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic and moderately halophilic bacterium, designated strain EMB201T, was isolated from tidal flat sediment of the South Sea in Korea. Cells were motile rods with a single polar flagellum and had catalase- and oxidase-positive activities. Growth of strain EMB201T was observed at 15–37 °C (optimum, 30 °C), at pH 5.0–9.5 (optimum, pH 7.0–7.5) and in the presence of 1–7 % (w/v) NaCl (optimum, 2–3 %). Strain EMB201T contained ubiquinone-10 as the sole isoprenoid quinone and summed feature 8 (comprising C18 : 1ω7c/ω6c), C18 : 0ω7c 11-methyl and C10 : 0 3-OH as the major fatty acids. Phosphatidylglycerol and an unidentified amino lipid were identified as the major polar lipids and an unidentified phospholipid and three unidentified lipids were detected as minor components. The G+C content of the genomic DNA was approximately 58.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain EMB201T formed a phylogenetic lineage with members of the genus Celeribacter. Strain EMB201T was related most closely to Celeribacter halophilus ZXM137T with a 16S rRNA gene sequence similarity of 98.3 %, and the level of DNA–DNA relatedness between the two strains was 17.0 ± 2.0 %. The combined chemotaxonomic and molecular properties suggest that strain EMB201T represents a novel species of the genus Celeribacter, for which the name Celeribacter naphthalenivorans sp. nov. is proposed. The type strain is EMB201T ( = KACC 18393T = JCM 30679T).
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Affiliation(s)
- Young Taek Oh
- Department of Microbiology and Immunology, Yonsei University, Seoul 120-752, Republic of Korea
| | - Catherine Avedoza
- Department of Animal Science & Technology, Sunchon National University, Sunchon 540-742, Republic of Korea
| | - Sang-Suk Lee
- Department of Animal Science & Technology, Sunchon National University, Sunchon 540-742, Republic of Korea
| | - Sang Eun Jeong
- Department of Life Science, Chung-Ang University, Seoul 156-756, Republic of Korea
| | - Baolei Jia
- Department of Life Science, Chung-Ang University, Seoul 156-756, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 156-756, Republic of Korea
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8
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Wang L, Liu Y, Wang Y, Dai X, Zhang XH. Celeribacter manganoxidans sp. nov., a manganese-oxidizing bacterium isolated from deep-sea sediment of a polymetallic nodule province. Int J Syst Evol Microbiol 2015; 65:4180-4185. [PMID: 26303941 DOI: 10.1099/ijsem.0.000558] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, strictly aerobic, non-motile, rod-shaped, manganese-oxidizing bacterial strain, designated DY2-5T, was isolated from surface sediment of Pacific Clarion-Clipperton Fracture Zone (CCFZ). Growth occurred at 0-37 °C (optimum 28 °C), pH 6.5-9.0 (optimum pH 7.0-7.5) and in the presence of 1-11% (w/v) NaCl (optimum 3-4%). Phylogenetic analysis based on 16S rRNA gene sequences revealed that the novel strain was most closely related to Celeribacter halophilus ZXM137T with 96.13% sequence similarity, and had 16S rRNA gene sequence similarities in the range 93.89-95.87% with other species of the genus Celeribacter. The dominant fatty acids were summed feature 8 (C18:1ω7c and/or C18:1ω6c) and C16:0. The polar lipids of strain DY2-5T comprised phosphatidylglycerol, phosphatidylcholine and two unknown aminolipids. The major respiratory quinone was ubiquinone-10 (Q-10). The DNA G+C content of strain DY2-5T was 64.8 mol%. On the basis of the phenotypic, genotypic and physiological evidence, strain DY2-5T represents a novel species of the genus Celeribacter, for which the name Celeribacter manganoxidans sp. nov. is proposed. The type strain is DY2-5T ( = JCM 19384T = KCTC 32473T).
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Affiliation(s)
- Long Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Yan Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Yanan Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Xiaofeng Dai
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Xiao-Hua Zhang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
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9
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Schimpel C, Werzer O, Fröhlich E, Leitinger G, Absenger-Novak M, Teubl B, Zimmer A, Roblegg E. Atomic force microscopy as analytical tool to study physico-mechanical properties of intestinal cells. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2015. [PMID: 26199850 PMCID: PMC4505173 DOI: 10.3762/bjnano.6.151] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
The small intestine is a complex system that carries out various functions. The main function of enterocytes is absorption of nutrients, whereas membranous cells (M cells) are responsible for delivering antigens/foreign substances to the mucosal lymphoid tissues. However, to get a fundamental understanding of how cellular structures contribute to physiological processes, precise knowledge about surface morphologies, cytoskeleton organizations and biomechanical properties is necessary. Atomic force microscopy (AFM) was used here as a powerful tool to study surface topographies of Caco-2 cells and M cells. Furthermore, cell elasticity (i.e., the mechanical response of a cell on a tip indentation), was elucidated by force curve measurements. Besides elasticity, adhesion was evaluated by recording the attraction and repulsion forces between the tip and the cell surface. Organization of F-actin networks were investigated via phalloidin labeling and visualization was performed with confocal laser scanning fluorescence microscopy (CLSM) and scanning electron microscopy (SEM). The results of these various experimental techniques revealed significant differences in the cytoskeleton/microvilli arrangements and F-actin organization. Caco-2 cells displayed densely packed F-actin bundles covering the entire cell surface, indicating the formation of a well-differentiated brush border. In contrast, in M cells actins were arranged as short and/or truncated thin villi, only available at the cell edge. The elasticity of M cells was 1.7-fold higher compared to Caco-2 cells and increased significantly from the cell periphery to the nuclear region. Since elasticity can be directly linked to cell adhesion, M cells showed higher adhesion forces than Caco-2 cells. The combination of distinct experimental techniques shows that morphological differences between Caco-2 cells and M cells correlate with mechanical cell properties and provide useful information to understand physiological processes/mechanisms in the small intestine.
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Affiliation(s)
- Christa Schimpel
- Institute of Pharmaceutical Sciences, Department of Pharmaceutical Technology, NAWI Graz, Karl-Franzens-University of Graz, BioTechMed-Graz, Austria
| | - Oliver Werzer
- Institute of Pharmaceutical Sciences, Department of Pharmaceutical Technology, NAWI Graz, Karl-Franzens-University of Graz, BioTechMed-Graz, Austria
| | - Eleonore Fröhlich
- Medical University of Graz, Center for Medical Research, BioTechMed-Graz, Austria
| | - Gerd Leitinger
- Research Unit Electron Microscopic Techniques, Institute of Cell Biology, Histology and Embryology, Center for Medical Research, Medical University of Graz, BioTechMed-Graz, Austria
| | | | - Birgit Teubl
- Institute of Pharmaceutical Sciences, Department of Pharmaceutical Technology, NAWI Graz, Karl-Franzens-University of Graz, BioTechMed-Graz, Austria
| | - Andreas Zimmer
- Institute of Pharmaceutical Sciences, Department of Pharmaceutical Technology, NAWI Graz, Karl-Franzens-University of Graz, BioTechMed-Graz, Austria
| | - Eva Roblegg
- Institute of Pharmaceutical Sciences, Department of Pharmaceutical Technology, NAWI Graz, Karl-Franzens-University of Graz, BioTechMed-Graz, Austria
- Research Center Pharmaceutical Engineering GmbH, Graz, Austria
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Celeribacter indicus sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium from deep-sea sediment and reclassification of Huaishuia halophila as Celeribacter halophilus comb. nov. Int J Syst Evol Microbiol 2014; 64:4160-4167. [DOI: 10.1099/ijs.0.069039-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A taxonomic study was carried out on strain P73T, which was isolated from deep-sea sediment of the Indian Ocean by enrichment of polycyclic aromatic hydrocarbons. The strain was able to degrade biphenyl, naphthalene, 2-methylnaphthalene, 2,6-dimethylnaphthalene, acenaphthene, anthracene, phenanthrene, dibenzothiophene, dibenzofuran, fluorene, 4-methyldibenzothiophene and fluoranthene, but not pyrene or chrysene. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain P73T formed a clade with the genera
Celeribacter
and
Huaishuia
within the family
Rhodobacteraceae
, with highest sequence similarity of 96.98 % to
Celeribacter neptunius
H 14T, followed by
Huaishuia halophila
ZXM137T (96.42 %). The bacterium was Gram-stain-negative, oxidase- and catalase-positive, rod-shaped and non-motile. Growth was observed at salinities from 0.5 to 12 % and at temperatures from 10 to 41 °C. The principal fatty acids (>10 %) of strain P73T were summed feature 8 (C18 : 1ω7c/ω6c) and C19 : 0ω8c cyclo. The sole respiratory quinone was Q-10. The major lipids were phosphatidylglycerol, one unknown aminolipid, one unknown phospholipid and one unknown lipid; a second unknown phospholipid and one unknown glycolipid were present as minor components. The G+C content of the chromosomal DNA was 66.0 mol%. The combined genotypic and phenotypic data show that strain P73T represents a novel species of the genus
Celeribacter
, for which the name Celeribacter indicus sp. nov. is proposed. The type strain is P73T ( = MCCC 1A01112T = LMG 27600T = DSM 27257T). Phylogenetic study and existing phenotypic information also show that
Huaishuia halophila
should be transferred to the genus
Celeribacter
as Celeribacter halophilus comb. nov. (type strain ZXM137T = MCCC 1A06432T = CGMCC 1.8891T = LMG 24854T).
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11
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Amylibacter marinus gen. nov., sp. nov., isolated from surface seawater. Int J Syst Evol Microbiol 2014; 64:4016-4020. [DOI: 10.1099/ijs.0.065847-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, non-motile, mesophilic, aerobic, rod-shaped bacterium, designated strain 2-3T, was isolated from surface seawater at Muroto city, Kochi prefecture, Japan. This strain grew well with starch. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain fell within the family
Rhodobacteraceae
and that the strain was related most closely to the genus
Pacificibacter
(94.0 % sequence similarity to the type strain). The DNA G+C content was 52.4 mol%. The major fatty acids were C18 : 1ω7c, C14 : 0 and C16 : 0. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, one unidentified lipid, one unidentified aminolipid and one unidentified phospholipid. The major isoprenoid quinone was Q-10. Strain 2-3T did not grow at 4 or 35 °C, while the type strain of the type species of the genus
Pacificibacter
grows at both temperatures. From the taxonomic data obtained in this study, it is proposed that strain 2-3T be placed into a novel genus and species named Amylibacter marinus gen. nov., sp. nov. in the family
Rhodobacteraceae
. The type strain of Amylibacter marinus is 2-3T ( = NBRC 110140T = LMG 28364T).
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12
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Baek K, Choi A, Kang I, Cho JC. Celeribacter marinus sp. nov., isolated from coastal seawater. Int J Syst Evol Microbiol 2014; 64:1323-1327. [PMID: 24425746 DOI: 10.1099/ijs.0.060673-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-negative, non-motile, non-pigmented and rod-shaped bacterial strain, designated IMCC12053(T), was isolated from coastal surface seawater of the Yellow Sea, Korea. Optimal growth of strain IMCC12053(T) was observed at 30 °C, pH 7.0 and in the presence of 2 % (w/v) NaCl. 16S rRNA gene sequence comparisons showed that strain IMCC12053(T) was most closely related to Celeribacter baekdonensis L-6(T) (97.5 % similarity) and Celeribacter neptunius H 14(T) (96.0 %). Strain IMCC12053(T) formed a robust phylogenetic clade with members of the genus Celeribacter. The DNA-DNA relatedness value between IMCC12053(T) and C. baekdonensis was far lower than 70 % (35.7-42.5 %), which indicated that strain IMCC12053(T) is a novel genomic species of the genus Celeribacter. The major respiratory isoprenoid quinone was ubiquinone-10 (Q-10) and major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine and aminolipids. The DNA G+C content was 61.0 mol%. On the basis of genotypic and phenotypic data collected in this study, it is proposed that strain IMCC12053(T) represents a novel species of the genus Celeribacter, for which the name Celeribacter marinus sp. nov. is proposed. The type strain is IMCC12053(T) ( = KACC 17482(T) = NBRC 109702(T)).
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Affiliation(s)
- Kiwoon Baek
- Department of Biological Sciences, Inha University, Incheon 402-751, Republic of Korea
| | - Ahyoung Choi
- Department of Biological Sciences, Inha University, Incheon 402-751, Republic of Korea
| | - Ilnam Kang
- Department of Biological Sciences, Inha University, Incheon 402-751, Republic of Korea
| | - Jang-Cheon Cho
- Department of Biological Sciences, Inha University, Incheon 402-751, Republic of Korea
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Yoon JH, Park S, Jung YT. Aestuariihabitans beolgyonensis gen. nov., sp. nov., a novel alphaproteobacterium isolated from tidal flat sediment. Antonie van Leeuwenhoek 2013; 104:217-24. [DOI: 10.1007/s10482-013-9940-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 05/24/2013] [Indexed: 11/28/2022]
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14
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Description of Litoreibacter meonggei sp. nov., isolated from the sea squirt Halocynthia roretzi, reclassification of
Thalassobacter arenae
as Litoreibacter arenae comb. nov. and emended description of the genus
Litoreibacter
Romanenko et al. 2011. Int J Syst Evol Microbiol 2012; 62:1825-1831. [DOI: 10.1099/ijs.0.035113-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, non-motile and coccoid, ovoid or rod-shaped bacterial strain, designated MA1-1T, was isolated from a sea squirt (Halocynthia roretzi) collected from the South Sea, Korea. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain MA1-1T is phylogenetically closely related to
Litoreibacter
species and to
Thalassobacter arenae
. It exhibited 16S rRNA gene sequence similarities of 97.3, 97.1 and 97.3 % to the type strains of
Litoreibacter albidus
,
Litoreibacter janthinus
and
T. arenae
, respectively. Strain MA1-1T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the predominant fatty acid. The polar lipid profile of strain MA1-1T was similar to those of the type strains of
L. albidus
and
L. janthinus
.
T. arenae
was found to be phylogenetically and chemotaxonomically more closely related to
Litoreibacter
species and strain MA1-1T than to
Thalassobacter stenotrophicus
, the type species of the genus
Thalassobacter
. The DNA G+C content of strain MA1-1T was 57.9 mol%, and DNA–DNA relatedness to the type strains of the two
Litoreibacter
species and
T. arenae
was 9–14 %. Differential phenotypic properties, together with the observed phylogenetic and genetic distinctiveness, distinguished strain MA1-1T from the two
Litoreibacter
species and
T. arenae
. On the basis of the data presented, strain MA1-1T is considered to represent a novel species of the genus
Litoreibacter
, for which the name Litoreibacter meonggei sp. nov. is proposed. The type strain is MA1-1T ( = KCTC 23699T = CCUG 61486T). In this study, it is also proposed that
Thalassobacter arenae
is reclassified as a member of the genus
Litoreibacter
, Litoreibacter arenae comb. nov. (type strain GA2-M15T = DSM 19593T = KACC 12675T). An emended description of the genus
Litoreibacter
is also presented.
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Liu K, Zong R, Li Q, Fu Y, Xu Y, Wang Y, Jiao N. Oceaniovalibus guishaninsula gen. nov., sp. nov., A Marine Bacterium of the Family Rhodobacteraceae. Curr Microbiol 2012; 64:385-91. [DOI: 10.1007/s00284-012-0081-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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16
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Wang H, Zhang X, Yan S, Qi Z, Yu Y, Zhang XH. Huaishuia halophila gen. nov., sp. nov., isolated from coastal seawater. Int J Syst Evol Microbiol 2012; 62:223-228. [DOI: 10.1099/ijs.0.025536-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-negative, non-motile bacterium, designated ZXM137T, was isolated from seawater collected from a coastal region of Qingdao, China, during a massive green algae (Enteromorpha prolifera) bloom. Strain ZXM137T was strictly aerobic and did not accumulate poly-β-hydroxybutyrate. Growth occurred with 0.5–11.0 % (w/v) NaCl, at pH 6–9 (optimum of pH 7) and at 4–45 °C (optimum at 28 °C). It contained Q-10 as the predominant ubiquinone and the major polar lipids were phosphatidylglycerol, phospholipids, and an unidentified aminolipid and lipid. The major cellular fatty acids of strain ZXM137T were C18 : 1ω7c, C18 : 1ω6c and 11-methyl C18 : 1ω7c. The DNA G+C content was 60.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain ZXM137T formed a distinct evolutionary lineage within the Roseobacter group in the class Alphaproteobacteria. On the basis of phenotypic, chemotaxonomic and phylogenetic evidence, strain ZXM137T represents a novel species in a new genus, for which the name Huaishuia halophila gen. nov., sp. nov. is proposed; the type strain is ZXM137T ( = CGMCC 1.8891T = LMG 24854T).
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Affiliation(s)
- Hong Wang
- Key Laboratory of Marine Genetics and Breeding for Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, PR China
| | - Xiuming Zhang
- Key Laboratory of Marine Genetics and Breeding for Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, PR China
| | - Shulin Yan
- Key Laboratory of Marine Genetics and Breeding for Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, PR China
| | - Zizhong Qi
- Key Laboratory of Marine Genetics and Breeding for Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, PR China
| | - Yong Yu
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, PR China
| | - Xiao-Hua Zhang
- Key Laboratory of Marine Genetics and Breeding for Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, PR China
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Lee SY, Park S, Oh TK, Yoon JH. Celeribacter baekdonensis sp. nov., isolated from seawater, and emended description of the genus Celeribacter Ivanova et al. 2010. Int J Syst Evol Microbiol 2011; 62:1359-1364. [PMID: 21828017 DOI: 10.1099/ijs.0.032227-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, non-motile, ovoid or rod-shaped bacterial strain, designated L-6(T), was isolated from seawater of Baekdo harbour of the East Sea in Korea and its taxonomic position was investigated by using a polyphasic study. Strain L-6(T) grew optimally at 30 °C, at pH 7.5-8.0 and in the presence of 2 % (w/v) NaCl. In the neighbour-joining phylogenetic tree based on 16S rRNA gene sequences, strain L-6(T) formed a cluster with the type strain of Celeribacter neptunius at a bootstrap resampling value of 100 %. Strain L-6(T) exhibited 16S rRNA gene sequence similarity values of 97.7 % to C. neptunius H 14(T) and of less than 96.2 % to the type strains of other species used in the phylogenetic analysis. The G+C content of the chromosomal DNA of strain L-6(T) was 60.9 mol%. The predominant ubiquinone found in strain L-6(T) and C. neptunius CIP 109922(T) was ubiquinone-10 (Q-10). The predominant fatty acid of strain L-6(T) and C. neptunius CIP 109922(T) was C(18:1)ω7c. The major polar lipids of strain L-6(T) were phosphatidylglycerol, one unidentified aminolipid and one unidentified lipid. The mean level of DNA-DNA relatedness between strain L-6(T) and C. neptunius CIP 109922(T) was 17 %. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, demonstrated that strain L-6(T) is distinguishable from C. neptunius. On the basis of the data presented, strain L-6(T) is considered to represent a novel species of the genus Celeribacter, for which the name Celeribacter baekdonensis sp. nov. is proposed. The type strain is L-6(T) ( = KCTC 23497(T) = CCUG 60799(T)).
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Affiliation(s)
- Soo-Young Lee
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yuseong, Daejeon, Republic of Korea
| | - Sooyeon Park
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yuseong, Daejeon, Republic of Korea
| | - Tae-Kwang Oh
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yuseong, Daejeon, Republic of Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
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Physico-mechanical characterisation of cells using atomic force microscopy — Current research and methodologies. J Microbiol Methods 2011; 86:131-9. [DOI: 10.1016/j.mimet.2011.05.021] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Revised: 05/18/2011] [Accepted: 05/26/2011] [Indexed: 11/21/2022]
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Vadicella arenosi gen. nov., sp. nov., a Novel Member of the Class Alphaproteobacteria Isolated from Sandy Sediments from the Sea of Japan Seashore. Curr Microbiol 2010; 62:795-801. [DOI: 10.1007/s00284-010-9780-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Accepted: 09/16/2010] [Indexed: 10/18/2022]
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