Inaccurate viral prediction leads to overestimated diversity of the archaeal virome in the human gut

Moissl-Eichinger, C. et al. Archaea are interactive components of complex microbiomes. Trends Microbiol. 26, 70–85 (2018).Article 
CAS 
PubMed 

Google Scholar 
Li, R., Wang, Y., Hu, H., Tan, Y. & Ma, Y. Metagenomic analysis reveals unexplored diversity of archaeal virome in the human gut. Nat. Commun. 13, 7978 (2022).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Gregory et al. The gut virome database reveals age-dependent patterns of virome diversity in the human gut. Cell Host Microbe. 28, 724–740.e8 (2020).Nayfach, S. et al. Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome. Nat. Microbiol. 6, 960–970 (2021 a).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Chibani, C. M. et al. A catalogue of 1,167 genomes from the human gut archaeome. Nat. Microbiol. 7, 48–61 (2022).Article 
CAS 
PubMed 

Google Scholar 
Nayfach, S. et al. CheckV assesses the quality and completeness of metagenome-assembled viral genomes. Nat. Biotechnol. 39, 578–585 (2021 b).Article 
CAS 
PubMed 

Google Scholar 
Camargo, A. P. et al. Identification of mobile genetic elements with geNomad. Nat. Biotechnol. https://doi.org/10.1038/s41587-023-01953-y (2023).Kieft, K., Zhou, Z. & Anantharaman, K. VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences. Microbiome 8, 1–23 (2020).Article 

Google Scholar 
Antipov, D., Raiko, M., Lapidus, A. & Pevzner, P. A. Metaviral SPAdes: assembly of viruses from metagenomic data. Bioinformatics 36, 4126–4129 (2020).Article 
CAS 
PubMed 

Google Scholar 
Roux, S., Enault, F., Hurwitz, B. L. & Sullivan, M. B. VirSorter: mining viral signal from microbial genomic data. PeerJ 3, e985 (2015).Article 
PubMed 
PubMed Central 

Google Scholar 
Guo, J. et al. VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses. Microbiome 9, 1–13 (2021).Article 

Google Scholar 
Paez-Espino, D. et al. Uncovering earth’s virome. Nature 536, 425–430 (2016).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Shmakov, S. A. et al. The CRISPR spacer space is dominated by sequences from species-specific mobilomes. mBio 8, e01397–17 (2017).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Wagner, A. et al. Mechanisms of gene flow in archaea. Nat. Rev. Microbiol. 15, 492–501 (2017).Article 
CAS 
PubMed 

Google Scholar 
Atanasova, N. S., Roine, E., Oren, A., Bamford, D. H. & Oksanen, H. M. Global network of specific virus–host interactions in hypersaline environments. Environ. Microbiol. 14, 426–440 (2012).Article 
CAS 
PubMed 

Google Scholar 
Conant, G. C. & Wolfe, K. H. GenomeVx: simple web-based creation of editable circular chromosome maps. Bioinformatics 24, 861–862 (2008).Article 
CAS 
PubMed 

Google Scholar