Biases in viral metagenomics-based detection, cataloguing and quantification of bacteriophage genomes in human faeces, a review
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Published Version
Supplementary Materials
Date
2021
Authors
Callanan, Julie
Stockdale, Stephen R.
Shkoporov, Andrey N.
Draper, Lorraine A.
Ross, R. Paul
Hill, Colin
Journal Title
Journal ISSN
Volume Title
Publisher
MDPI
Published Version
Abstract
The human gut is colonised by a vast array of microbes that include bacteria, viruses, fungi, and archaea. While interest in these microbial entities has largely focused on the bacterial constituents, recently the viral component has attracted more attention. Metagenomic advances, compared to classical isolation procedures, have greatly enhanced our understanding of the composition, diversity, and function of viruses in the human microbiome (virome). We highlight that viral extraction methodologies are crucial in terms of identifying and characterising communities of viruses infecting eukaryotes and bacteria. Different viral extraction protocols, including those used in some of the most significant human virome publications to date, have introduced biases affecting their a overall conclusions. It is important that protocol variations should be clearly highlighted across studies, with the ultimate goal of identifying and acknowledging biases associated with different protocols and, perhaps, the generation of an unbiased and standardised method for examining this portion of the human microbiome.
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Keywords
Bacteriophage , Viral metagenomics , Phageome , Viral extraction
Citation
Callanan, J., Stockdale, S.R., Shkoporov, A., Draper, L.A., Ross, R.P. and Hill, C. (2021) ‘Biases in viral metagenomics-based detection, cataloguing and quantification of bacteriophage genomes in human faeces, a review’, Microorganisms, 9(3), 524 (15pp). doi: 10.3390/microorganisms9030524