COMPARATIVE METAGENOMICS ANALYSIS OF PALM OIL MILL EFFLUENT (POME) USING THREE DIFFERENT BIOINFORMATICS PIPELINES
The substantial cost reduction and massive production of next-generation sequencing (NGS) data have contributed to the progress in the rapid growth of metagenomics. However, production of the massive amount of data by NGS has revealed the challenges in handling the existing bioinformatics tools rela...
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| Published in: | IIUM engineering journal Vol. 20; no. 1; pp. 1 - 11 |
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| Main Authors: | , , , , |
| Format: | Journal Article |
| Language: | English |
| Published: |
IIUM Press, International Islamic University Malaysia
01-06-2019
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| Subjects: | |
| Online Access: | Get full text |
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| Summary: | The substantial cost reduction and massive production of next-generation sequencing (NGS) data have contributed to the progress in the rapid growth of metagenomics. However, production of the massive amount of data by NGS has revealed the challenges in handling the existing bioinformatics tools related to metagenomics. Therefore, in this research we have investigated an equal set of DNA metagenomics data from palm oil mill effluent (POME) sample using three different freeware bioinformatics pipelines’ websites of metagenomics RAST server (MG-RAST), Integrated Microbial Genomes with Microbiome Samples (IMG/M) and European Bioinformatics Institute (EBI) Metagenomics, in term of the taxonomic assignment and functional analysis. We found that MG-RAST is the quickest among these three pipelines. However, in term of analysis of results, IMG/M provides more variety of phylum with wider percent identities for taxonomical assignment and IMG/M provides the highest carbohydrates, amino acids, lipids, and coenzymes transport and metabolism functional annotation beside the highest in total number of glycoside hydrolase enzymes. Next, in identifying the conserved domain and family involved, EBI Metagenomics would be much more appropriate. All the three bioinformatics pipelines have their own specialties and can be used alternately or at the same time based on the user’s functional preference.
ABSTRAK: Pengurangan kos dalam skala besar dan pengeluaran data ‘next-generation sequencing’ (NGS) secara besar-besaran telah menyumbang kepada pertumbuhan pesat metagenomik. Walau bagaimanapun, pengeluaran data dalam skala yang besar oleh NGS telah menimbulkan cabaran dalam mengendalikan alat-alat bioinformatika yang sedia ada berkaitan dengan metagenomik. Justeru itu, dalam kajian ini, kami telah menyiasat satu set data metagenomik DNA yang sama dari sampel effluen kilang minyak sawit dengan menggunakan tiga laman web bioinformatik percuma iaitu dari laman web ‘metagenomics RAST server’ (MG-RAST), ‘Integrated Microbial Genomes with Microbiome Samples’ (IMG/M) dan ‘European Bioinformatics Institute’ (EBI) Metagenomics dari segi taksonomi dan analisis fungsi. Kami mendapati bahawa MG-RAST ialah yang paling cepat di antara ketiga-tiga ‘pipeline’, tetapi mengikut keputusan analisa, IMG/M mengeluarkan maklumat philum yang lebih pelbagai bersama peratus identiti yang lebih luas berbanding yang lain untuk pembahagian taksonomi dan IMG/M juga mempunyai bacaan tertinggi dalam hampir semua anotasi fungsional karbohidrat, amino asid, lipid, dan koenzima pengangkutan dan metabolisma malah juga paling tinggi dalam jumlah enzim hidrolase glikosida. Kemudian, untuk mengenal pasti ‘domain’ terpelihara dan keluarga yang terlibat, EBI metagenomics lebih bersesuaian. Ketiga-tiga saluran ‘bioinformatics pipeline’ mempunyai keistimewaan mereka yang tersendiri dan boleh digunakan bersilih ganti dalam masa yang sama berdasarkan pilihan fungsi penggun. |
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| ISSN: | 1511-788X 2289-7860 |
| DOI: | 10.31436/iiumej.v20i1.909 |