Virome Sequencing of Stool Samples

  • Lenka Kramná
  • Ondřej CinekEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1838)


Next-generation sequencing has opened avenues to studying complex populations such as the bacteriome (all bacteria), mycobiome (all fungi), and virome (all viruses in a given sample). Viromes are less often investigated as compared to bacteriomes. The reasons are mostly methodological: because no common pan-viral sequence signature exists, metagenomic sequencing remains the only option. This brings about the need of laborious virus enrichment, multiple signal amplification steps with virtually no possibility of interim quality control, and complicated bioinformatic analysis of the ensuing sequence data. Nevertheless, over the past decade virome sequencing has been enormously successful in identifying new agents in human and animal diseases, and in characterizing viruses in various ecological niches. Recently, virome sequencing has been also employed in studies of non-infectious diseases, which has brought about new challenges of sensitivity, costs, and reproducibility in testing of large sets of samples. Here, we present a detailed protocol that has been utilized in virome studies where hundreds of samples had to be reliably tested in order to assess the association of the stool virome with susceptibility to type 1 diabetes, a non-infectious autoimmune disease.

Key words

Metagenome Virus Bacteriophage Stool 



The development of the protocols was supported by Ministry of Health of the Czech Republic: grants nr. 15-31426A and 15-29078A to Charles University in Prague.


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Pediatrics, Second Faculty of MedicineCharles UniversityPragueCzech Republic
  2. 2.Department of Medical Microbiology, Second Faculty of MedicineCharles UniversityPragueCzech Republic

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