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Biases in Viral Metagenomics-Based Detection, Cataloguing and Quantification of Bacteriophage Genomes in Human Faeces, a Review

APC Microbiome Ireland and School of Microbiology, University College Cork, T12 YT20 Cork, Ireland
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Academic Editor: Elisabetta Caselli
Microorganisms 2021, 9(3), 524; https://doi.org/10.3390/microorganisms9030524
Received: 29 January 2021 / Revised: 17 February 2021 / Accepted: 2 March 2021 / Published: 4 March 2021
(This article belongs to the Special Issue Comparative Genomics of the Human Gut Microbiome)
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. View Full-Text
Keywords: bacteriophage; viral metagenomics; phageome; viral extraction bacteriophage; viral metagenomics; phageome; viral extraction
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MDPI and ACS Style

Callanan, J.; Stockdale, S.R.; Shkoporov, A.; Draper, L.A.; Ross, R.P.; Hill, C. Biases in Viral Metagenomics-Based Detection, Cataloguing and Quantification of Bacteriophage Genomes in Human Faeces, a Review. Microorganisms 2021, 9, 524. https://doi.org/10.3390/microorganisms9030524

AMA Style

Callanan J, Stockdale SR, Shkoporov A, Draper LA, Ross RP, Hill C. Biases in Viral Metagenomics-Based Detection, Cataloguing and Quantification of Bacteriophage Genomes in Human Faeces, a Review. Microorganisms. 2021; 9(3):524. https://doi.org/10.3390/microorganisms9030524

Chicago/Turabian Style

Callanan, Julie; Stockdale, Stephen R.; Shkoporov, Andrey; Draper, Lorraine A.; Ross, R. P.; Hill, Colin. 2021. "Biases in Viral Metagenomics-Based Detection, Cataloguing and Quantification of Bacteriophage Genomes in Human Faeces, a Review" Microorganisms 9, no. 3: 524. https://doi.org/10.3390/microorganisms9030524

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