High Quality of Bacterial DNA Extraction from Corbicula fluminea Tissue in Kelantan
DOI:
https://doi.org/10.11113/mjfas.v16n2.1503Keywords:
Corbicula fluminea, high quality DNA, modified CTAB, bacterial metagenome DNA extractionAbstract
Corbicula fluminea served as a popular traditional food in Kelantan, Malaysia. This clam is highly consumed by the local people from the last decade. However, there is lack of the study that obtain high quality of bacterial metagenome deoxyribonucleic acid (DNA) extraction from C. fluminea. Improper DNA extraction protocol always fails to extract a high integrity of bacterial DNA bands. This study compares the effectiveness and efficiency of conventional cetyltrimethylammonium bromide (CTAB) protocol, a commercial kit and modified CTAB protocol for bacterial DNA extraction from the soft tissue surface of raw C. fluminea. The instruments used to examine the quality of the extracted bacterial DNA were DeNovix DS-11 spectrophotometer, gel electrophoresis machine and UV transilluminator. The results showed that the bacterial DNA extracted from modified CTAB protocol the highest purity and integrity with the A₂₆₀/A₂₈₀ ratio of 1.92 ± 0.01 as well as the DNA band with minimum smear. This conclude that modified CTAB protocol is the best among the three extraction protocols for the bacterial extraction from the C. fluminea.
References
E.R. Aweng, A.A. Kutty, Etak, lokan air tawar. Dewan Bahasa dan Pustaka, 2018.
E.R. Aweng, M. Mohamed, Water quality and shellfish related gastrointestinal disease cases in Kota Bharu, Kelantan, Malaysia. Journal of Bioentrepreneurship, 1(2011), 9-13.
E.J. Stewart, Growing unculturable bacteria. J. Bacteriol., 194(2012), 4151-4160.
E.G. Zoetendal, C.T. Collier, S. Koike, R.I. Mackie, H.R. Gaskins, Molecular ecological analysis of the gastrointestinal microbiota: A review. J. Nutr., 134(2004), 465-472.
P.F. Thomsen, E. Willerslev, Environmental DNA - An emerging tool in conservation for monitoring past and present biodiversity. Biol. Conserv., 183(2015), 4-18.
C. Gill, J.H.H.M. van de Wijgert, F. Blow, A.C. Darby, Evaluation of lysis methods for the extraction of bacterial DNA for analysis of the vaginal microbiota. PloS One, 11(2016), e0163148. doi:10.1371/journal.pone.0163148
Z. Han, J. Sun, A. Lv, A. Wang, Biases from different DNA extraction methods in intestine microbiome research based on 16S rDNA sequencing: A case in the koi carp, Cyprinus carpio var. Koi. MicrobiologyOpen, 2018, e00626.
A. Vesty, K. Biswas, M.W. Taylor, K. Gear, R.G. Douglas, Evaluating the impact of DNA extraction method on the representation of human oral bacterial and fungal communities. PloS One, 12(2017), e0169877.
F. Aranishi, T. Okimoto, A simple and reliable method for DNA extraction from bivalve mantle. J. Appl. Genet., 47(2006), 251-254.
G. Hernández‐Zárate, J. Olmos‐Soto, Identification of bacterial diversity in the oyster Crassostrea gigas by fluorescent in situ hybridization and polymerase chain reaction. J. Appl. Microbiol., 100(2006), 664-672.
N. Trabal Fernández, J.M. Mazón-Suástegui, R. Vázquez-Juárez, F. Ascencio-Valle, J. Romero, Changes in the composition and diversity of the bacterial microbiota associated with oysters (Crassostrea corteziensis, Crassostrea gigas and Crassostrea sikamea) during commercial production. FEMS Microbiol. Ecol., 88(2014), 69-83. doi:10.1111/1574-6941.12270
D.C.A. Leite, F.C. Balieiro, C.A. Pires, B.E. Madari, A.S. Rosado, H.L.C. Coutinho, R.S. Peixoto, Comparison of DNA extraction protocols for microbial communities from soil treated with biochar. Braz. J. Microbiol., 45(2014), 175-183. https://dx.doi.org/10.1590/S1517-83822014000100023
A. Psifidi, et al., Comparison of eleven methods for genomic DNA extraction suitable for large-scale whole-genome genotyping and long-term DNA banking using blood samples. PloS One 10(2015): e0115960. https://doi.org/10.1371/journal.pone.0115960
J.F. Gomes, et al. Biofiltration using C. fluminea for E. coli removal from water: Comparison with ozonation and photocatalytic oxidation. Chemosphere, 208(2018), 674-681
K. Wilson, Preparation of genomic DNA from bacteria current protocols in molecular biology: John Wiley & Sons, Inc. 2001
G. Lucena-Aguilar, A.M. Sánchez-López, C. Barberán-Aceituno, J.A. Carrillo-Avila, J.A. López-Guerrero, R. Aguilar-Quesada, DNA source selection for downstream applications based on DNA quality indicators analysis. Biopreserv. Biobank., 14(2016), 264-270.
J. Sambrook, D.W. Russell, Molecular cloning: A laboratory manual. third. Cold pring Harbor Laboratory Press, New York. 2001
I. Djurkin Kušec, Ž. Radišić, M. Komlenić, G. Kušec, Comparison of commercial DNA Kits and traditional DNA extraction procedure in PCR detection of pork in dry/fermented sausages. PoljoPrivreda, 21(2015), 199-202.
R. Kuhn, J. Böllmann, K. Krahl, I. M. Bryant, M. Martienssen, Comparison of ten different DNA extraction procedures with respect to their suitability for environmental samples. J. Microbiol. Methods., 143(2017), 78-86.
S. El-Ashram, I. Al Nasr, X. Suo, Nucleic acid protocols: Extraction and optimization. Biotechnol. Rep., 12(2016), 33-39. doi:https://doi.org/10.1016/j.btre.2016.10.001
P.Y. Lee, J. Costumbrado, C.-Y. Hsu, Y.H. Kim, Agarose gel electrophoresis for the separation of DNA fragments. J. Vis. Exp., 62(2012).
T. Klingstrom, E. Bongcam-Rudloff, O. V. Pettersson, A comprehensive model of DNA fragmentation for the preservation of high molecular weight DNA. BioRxiv, 2018, 254276.
G.B. Barra, et.al., EDTA-mediated inhibition of DNases protects circulating cell-free DNA from ex vivo degradation in blood samples. Clin. Biochem., 48 (2015), 976-981. 10.1016/j.clinbiochem.2015.02.014
M. Alimolaei, M. Golchin, An efficient DNA extraction method for Lactobacillus casei, a difficult-to-lyse bacterium. Int. J. Enteric. Pathog., 4(2016), 1-6.
L.K. Hallmaier-Wacker, S. Lueert, C. Roos, S. Knauf, The impact of storage buffer, DNA extraction method, and polymerase on microbial analysis. Sci. rep., 8(2018), 6292-6292. doi:10.1038/s41598-018-24573-y
