RT Journal Article
SR Electronic
T1 A step-by-step sequence-based analysis of virome enrichment protocol for freshwater and sediment samples
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.09.17.302836
DO 10.1101/2020.09.17.302836
A1 Federica Pinto
A1 Moreno Zolfo
A1 Francesco Beghini
A1 Federica Armanini
A1 Francesco Asnicar
A1 Andrea Silverj
A1 Adriano Boscaini
A1 Nico Salmaso
A1 Nicola Segata
YR 2020
UL http://biorxiv.org/content/early/2020/09/20/2020.09.17.302836.abstract
AB Cultivation-free metagenomic analysis afforded unprecedented details on the diversity, structure and potential functions of microbial communities in different environments. When employed to study the viral fraction of the community that is recalcitrant to cultivation, metagenomics can shed light into the diversity of viruses and their role in natural ecosystems. However, despite the increasing interest in virome metagenomics, methodological issues still hinder the proper interpretation and comparison of results across studies. Virome enrichment experimental protocols are key multi-step processes needed for separating and concentrating the viral fraction from the whole microbial community prior to sequencing. However, there is little information on their efficiency and their potential biases. To fill this gap, we used metagenomic and amplicon sequencing to examine the microbial community composition through the serial filtration and concentration steps commonly used to produce viral-enriched metagenomes. The analyses were performed on water and sediment samples from an Alpine lake. We found that, although the diversity of the retained microbial communities declined progressively during the serial filtration, the final viral fraction contained a large proportion (from 10% to 40%) of non-viral taxa, and that the efficacy of filtration showed biases based on taxonomy. Our results quantified the amount of bacterial genetic material in viromes and highlighted the influence of sample type on the enrichment efficacy. Moreover, since viral-enriched samples contained a significant portion of microbial taxa, computational sequence analysis should account for such biases in the downstream interpretation pipeline.Importance Filtration is a commonly used method to enrich viral particles in environmental samples. However, there is little information on its efficiency and potential biases on the final result. Using a sequence-based analysis on water and sediment samples, we found that filtration efficacy is dependent on sample type and that the final virome contained a large proportion of non-viral taxa. Our finding stressed the importance of downstream analysis to avoid biased interpretation of data.