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General Session 3: Biological oceanography & global change |
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Optimised sample quality for amplicon metagenomic sequencing
GS3-52
Swee Keong Yeap* , Xiamen University Malaysia
Jalan Sunsuria, Bandar Sunsuria,
43900 Sepang, Selangor Darul Ehsan
Shao Feng Mok, ScienceVision Sdn Bhd Setia Avenue, 33A-4 Jalan Setia Prima S, U13/S, Setia Alam, Seksyen U13, 40170 Shah Alam, Selangor Darul Ehsan, Malaysia
Sook Yee Boo, ScienceVision Sdn Bhd Setia Avenue, 33A-4 Jalan Setia Prima S, U13/S, Setia Alam, Seksyen U13, 40170 Shah Alam, Selangor Darul Ehsan, Malaysia
Woan Charn Nancy-Liew, Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
Sheau Wei Tan, Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
Presenter Email: skyeap@xmu.edu.my
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| Ocean acidification is a global issue contributed by the increasing atmospheric CO2 due to human activities. Stress caused by ocean acidification was found to create pressure on selection and shape the microbial diversity and activities in the marine ecosystems. To-date, attention was mainly focus on culturable microbes. However, various reports have shown that present and involvement of non-culturable microbes shall not be neglected. 16s amplicon metagenomic sequencing has been widely used to study the present of non-culturable microbes in the environmental samples. However, our previous experience have shown that this amplicon sequencing method encounter higher chances of failure comparing to the shotgun metagenomic sequencing. Present of PCR inhibitor was identified as the main contributor to the underestimation of the amplicon library concentration that cause overcluster of the amplicon sequencing. Several approaches including chemical and column methods, which were proposed as effective ways to remove PCR inhibitor, failed to achieve the objective. Cross comparison of the DNA extraction methods clearly indicated that effective DNA extraction plays the most important role to avoid failure of amplicon metagenomic sequencing. |
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