Funding

The project has been supported by:

to Nicola Segata

  • JST AIP Acceleration Research (JPMJCR19U3)
  • Japan Society for the Promotion of Science (KAKENHI JP16H06279 (PAGS)
to Takuji Yamada

  • SUKRI/MRC grants MR/W026813/1 and MR/Y010175/1
to Cristina Menni

Viral Sequence Clusters

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 page recapitulates our findings and points to the public collection of > 162,000 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).

 

Profiling Tool

The resource has been integrated in MetaPhlAn 4.1, that can now profile VSCs in metagenomes. If you want to use it, check out the MetaPhlan4 wiki and tutorials

Data repository

  • The full set of 162,876 reconstructed sequences is available here
  • The 47,820 representatives of each cluster are available here
  • The 45,872 representatives of each cluster, de-replicated at 99% identity are available here
  • The CRISPR virus-host assignments are available in the Supplementary Table 8 and also as CSV files here: VSG-to-SGBs and VSG-to-species
  • Additional data is available in Zenodo: here

Citation

If you use this resource in your research, please cite our preprint:

Moreno Zolfo 1,2 Andrea Silverj 1,3,4 Aitor Blanco-Míguez 1 Paolo Manghi 1 Omar Rota-Stabelli 1,3,4 Vitor Heidrich 1 Joardan Jensen5 Sagun Maharjan5 Eric Franzosa5 Cristina Menni 6 Alessia Visconti 7 Federica Pinto 1 Matteo Ciciani 1 Curtis Huttenhower5 Anna Cereseto 1 Francesco Asnicar 1 Hiroaki Kitano 2,8 Takuji Yamada 2,9,10,11,12 Nicola Segata 1,13

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

bioRxiv 2024 10.1101/2024.02.19.580813

1 Department CIBIO - University of Trento, Italy

2 Integrated Open Systems Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan

3 Center Agriculture Food Environment (C3A), University of Trento, Italy

4 Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy

5 Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA

6 Department of Twin Research & Genetic Epidemiology, King’s College London, London, UK

7 Center of Biostatistics, Epidemiology and Public Health, Department of Clinical and Biological Sciences, University of Turin, Turin, Italy

8 The Systems Biology Institute (SBI), Tokyo, Japan

9 School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan

10 Metagen, Inc., Yamagata, Japan

11 Metagen Therapeutics, Inc., Yamagata, Japan

12 Digzyme, Inc., Tokyo, Japan

13 Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy

Examples

You can download an example tutorial dataset and follow this bioBakery tutorial

Support & Contact

For comments and questions please contact us or visit the bioBakery Help Forum