Characterization of novel marine bacterium vitellibacter aquimaris using polyphasic approach and genomic analyses

dc.contributor.authorThevarajoo, Suganthi
dc.date.accessioned2023-05-15T04:50:13Z
dc.date.available2023-05-15T04:50:13Z
dc.date.issued2018
dc.descriptionThesis (PhD. (Biosciences))
dc.description.abstractThe discovery of novel marine bacteria provides an opportunity in exploring new bioactive compounds and their significance. Extensive industrial applications of enzymes promote the search of the enzymes from the new source. In this study, a yellow-orange strain designated as D-24 was isolated from Desaru, Johor. The study aimed to taxonomically and genomically characterize strain D-24 through polyphasic approach and genome analyses, respectively. The 16S rRNA gene sequence of strain D-24 indicated that it belongs to genus Vitellibacter. Strain D-24 was distinct from the other Vitellibacter spp. in hydrolyse Tween 60 and tyrosine, composition of fatty acids, polar lipid profile and DNA–DNA relatedness. Hence, strain D-24 was proposed as a new type strain with the name of Vitellibacter aquimaris. Following, strain D-24 was characterized on its protease activity and extracellular protease encoding genes. The characterization of crude protease demonstrated optimum activity at 60 °C, 5 % (w/v) NaCl and pH 7. The draft genome sequence of V. aquimaris (3.1 Mbp) was generated using an Illumina MiSeq sequencer. Mining of genes revealed the presence of three metalloproteases, two serine proteases and a cysteine protease. Recently, genus Vitellibacter was suggested as the same genus of Aequorivita based on phylogenomic data with no further analyses. Therefore, the detailed comparative analyses were performed based on their phenotypic and genomic features. Analyses of 16S rRNA gene sequences, housekeeping genes, percentage of conserved proteins and phenotypic features supported both of them as same genus. Furthermore, the presence of proteases, glycoside hydrolases and denitrification genes in genome of Vitellibacter/Aequorivita revealed their role in detergent industry, food industry and in carbon mineralization. In a nutshell, this study has provided new knowledge on V. aquimaris and also the useful genes such as serine protease, beta-mannosidase and nitrous oxide reductase that could be further characterized
dc.description.sponsorshipFaculty of Biosciences and Medical Engineering
dc.identifier.urihttp://openscience.utm.my/handle/123456789/421
dc.language.isoen
dc.publisherUniversiti Teknologi Malaysia
dc.subjectBiosciences and medical engineering
dc.titleCharacterization of novel marine bacterium vitellibacter aquimaris using polyphasic approach and genomic analyses
dc.typeThesis
dc.typeDataset
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Composition of media used in this study
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Maximum-likelihood tree based on 16S rRNA gene sequences showing the phylogenetic position of strain D-24 among the type strains of the genus Vitellibacter and other related taxa Table B Enzyme activity between strain D-24 and type strains of species of the genus Vitellibacter obtained from API ZYM Table B2 Carbon source utilization tested for strain D-24 species of the genus Vitellibacter using API 50 CH
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Predicted protein sequences (potentially involved in proteolytic activity) in the genome of V. aquimaris D-24T based on search in UniProt database Table C2 The protein sequence of six predicted protein sequences (with signal peptide) retrieved from the genome of V. aquimaris D-24T Table C3 The nucleotide sequence of Vap6 validated by sequencing using design primers
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The unique KO IDs found in the three Vitellibacter spp. genomes with respect to genes and their predicted function
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