Comparative metagenomics analysis of palm oil mill effluent (POME) using three different bioinformatics pipelines

Parman, Adibah and Mat Isa, Mohd Noor and Ben Belgacem, Farah Fadwa and Noorbatcha, Ibrahim Ali and Mohd. Salleh, Hamzah (2019) Comparative metagenomics analysis of palm oil mill effluent (POME) using three different bioinformatics pipelines. IIUM Engineering Journal, 20 (1). pp. 1-11. ISSN 1511-788X E-ISSN 2289-7860

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Abstract

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.

Item Type:	Article (Journal)
Additional Information:	3704/72529
Uncontrolled Keywords:	POME, metagenomics, glycoside hydrolase enzymes, IMG/M, EBI, MGI-RAST, NGS
Subjects:	T Technology > TP Chemical technology T Technology > TP Chemical technology > TP248.13 Biotechnology
Kulliyyahs/Centres/Divisions/Institutes (Can select more than one option. Press CONTROL button):	Kulliyyah of Engineering Kulliyyah of Engineering > Department of Biotechnology Engineering
Depositing User:	Prof. Dr. Ibrahim Ali Noorbatcha
Date Deposited:	11 Jun 2019 15:12
Last Modified:	23 Jul 2021 10:50
URI:	http://irep.iium.edu.my/id/eprint/72529

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