Discovering and exploring the hidden diversity of the human gut viruses using highly enriched virome samples.

Discovering and exploring the hidden diversity of the human gut viruses using highly enriched virome samples

Viruses are crucially important in the human microbiome. By leveraging enriched Viral-Like Particle (VLP) viromes, through metagenomic assembly and sequence clustering, we retrieved thousands of viral contigs by from viromes and metagenomes.This upload contains the public collection of > 162,000 viral sequnces we retrieved. Sequences are clustered into 3,944 VSCs (Viral Sequence Clusters) that are labelled as known (kVSCs) or unknown (uVSCs), and further grouped into 1,345 Viral Sequence Groups (VSGs).

Files

File
Description

VSC5_rep_fnas_nr99_45k_metaphlanDB.fna.gz
The 45,872 representative sequences (dereplicated at 99% identity), included in the MetaPhlan 4.1 module, in FASTA format.

VSCs_groups.csv
Metadata of the 45,872 representative sequences included in the MetaPhlan 4.1 module.

VSC5_rep_fnas_full_47k.fna.gz
The non-dereplicated set of  47,820 representative sequences.

VSC5_complete_162k_labelled.fna.gz

The complete set of 162,876 sequences of potential viral origin extracted from metagenomes and viromes:

5651 Highly Enriched Virome Contigs (HEVC)

126,894 contigs from the unbinned metagenomes of Pasolli et al.

30,331 contigs from viromes 

CRISPR_VSG-to-species.csv

CRISPR_VSG-to-SGBs.csv

The  host-associations of each VSG group (each line is a match between VSG-species and VSG-SGB).

VSC_profiling_examples.zip

An archive containing a test / tutorial subsampled dataset.

Supplementary Data

See Supplementary Figures and Tables in the original biorxiv publication.

Citation

Discovering and exploring the hidden diversity of the human gut viruses using highly enriched virome samples - bioRxiv 2024

Moreno Zolfo,  Andrea Silverj, Aitor Blanco-Míguez, Paolo Manghi, Omar Rota-Stabelli, Vitor Heidrich, Jordan Jensen, Sagun Maharjan, Eric Franzosa, Cristina Menni, Alessia Visconti, Federica Pinto, Matteo Ciciani, Curtis Huttenhower, Anna Cereseto, Francesco Asnicar, Hiroaki Kitano, Takuji Yamada, Nicola Segata.