Identification of the bacterium isolate from Mackerel Fish (Rastrelliger sp.) using 16S rRNA Gene

The use of probiotics in aquaculture can improve the quality and quantity of the fishes. One of potential probiotic bacterium from gastrointestine of mackerel fish (Rastrelliger sp.) isolated in this research were LUI-04. This study aimed to determine the species of bacterium isolate using nucleotid...

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Bibliographic Details
Published inIOP conference series. Earth and environmental science Vol. 293; no. 1; pp. 12043 - 12050
Main Authors Ismail, Y S, Febriani, Yulvizar, C, Ramadhani, R
Format Journal Article
LanguageEnglish
Published Bristol IOP Publishing 01.06.2019
Subjects
Aquaculture
Aquaculture techniques
Bacillus megaterium
Bacteria
controlling pathogenic microbes
Deoxyribonucleic acid
DNA
economic growth of fisheries
Electrophoresis
Homology
Mackerel
Microorganisms
Nucleotide sequence
Nucleotides
phylogenetic tree
Phylogeny
potencial probiotic bacteria
Probiotics
Rastrelliger
rRNA 16S
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Summary:The use of probiotics in aquaculture can improve the quality and quantity of the fishes. One of potential probiotic bacterium from gastrointestine of mackerel fish (Rastrelliger sp.) isolated in this research were LUI-04. This study aimed to determine the species of bacterium isolate using nucleotide sequence homology compared to other microorganisms in GenBank. The 16S rRNA genes of LUI-04 isolate were analyzed. The results of electrophoresis showed the DNA band had a size of 1 500 bp for amplification using Bact-27F and Uni-1492R primers, and about 250 bp to 500 bp with the Com-IF and Com-2R primers. The sequence of nucleotides was determined by Sanger method. The 16S rRNA sequence of the isolate and other bacteria in GenBank were compared with the Basic Alignment Search Tool (BLAST) to know the homology. Then, all of the sequences were aligned by ClustalW, and the phylogenetic tree was reconstructed with Neighbor Joining method using bootstrap analysis of 1 000 replicates. The results showed that LUI-04 had a homology of 99 % and the bootstrap value percentage of 86 % with Bacillus aryabhattai B8W22 and four strains of Bacillus megaterium (strain QM B1551, NBRC15308, strain IAM 13418 and ATCC 14581). Therefore, the LUI-04 isolate belongs to Bacillus megaterium species.
ISSN:1755-1307
1755-1315
DOI:10.1088/1755-1315/293/1/012043