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Diversity, composition, taxa biomarkers, and functional genes of fish gut microbes in peat swamp forests and its converted areas in North Selangor, Malaysia


Citation

Saadu, Hamidu and Sutra, Jumria and Ismail, Ahmad and Zulkifli, Syaizwan Zahmir and Amal, Mohammad Noor Azmai (2021) Diversity, composition, taxa biomarkers, and functional genes of fish gut microbes in peat swamp forests and its converted areas in North Selangor, Malaysia. Pertanika Journal of Tropical Agricultural Science, 44 (3). 617- 641. ISSN 1511-3701; ESSN: 2231-8542

Abstract

The aquatic organisms in peat swamp forests are under threat due to habitat degradation resulting from human activities. This study determines the fish gut microbes’ diversity, composition, taxa biomarkers, and functional genes in peat swamp forests and its converted areas in North Selangor, Malaysia. Three undisturbed and disturbed areas nearby the peat swamp forests were selected. First, the 16S amplicon metagenomic analysis was conducted to assess the composition and diversity of bacterial communities in fish gut contents from both areas. Then, Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) and Linear discriminant analysis Effect Size (LEfSe) were used to predict disease/pathogen related functional genes. This study revealed Proteobacteria, Firmicutes, Bacteroidetes, Fusobacteria, and Actinobacteria as the predominant phyla in both studied areas. In contrast, bacterial community profiles of disturbed and undisturbed areas were slightly dissimilar. Metagenome predictions revealed that genes are related to metabolism, environmental information processing, genetic information processing, cellular processes, human diseases, and organismal systems. Further investigation revealed six potential biomarker genes, including chronic myeloid leukaemia in an undisturbed area, Vibrio cholerae infection, bladder cancer, pathogenic Escherichia coli infection, Staphylococcus aureus infection, and pertussis in disturbed areas. This study revealed that the fish gut microbiome could be used as an indicator in comparing the undisturbed and disturbed ecosystems.


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Additional Metadata

Item Type: Article
Divisions: Faculty of Biotechnology and Biomolecular Sciences
Faculty of Science
Institute of Bioscience
DOI Number: https://doi.org/10.47836/pjtas.44.3.07
Publisher: Universiti Putra Malaysia Press
Keywords: Composition; Diversity; Fish gut microbes; Functional genes; Peat swamp forests; Taxa biomarkers
Depositing User: Ms. Nuraida Ibrahim
Date Deposited: 01 Nov 2021 22:04
Last Modified: 01 Nov 2021 22:04
Altmetrics: http://www.altmetric.com/details.php?domain=psasir.upm.edu.my&doi=10.47836/pjtas.44.3.07
URI: http://psasir.upm.edu.my/id/eprint/89036
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