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Communication Dans Un Congrès Année : 2016

Accessing virus genomes out of metagenomic data: improving statistical and bioinformatics analytic tools to better assess the contribution of phages on microbial ecosystems

Résumé

Many attempts to detect phages (bacterial viruses) in various microbial ecosystems have led to similar conclusions: (i) phages are present in all ecosystems where bacteria are present; (ii) but it remains hard to assess their contribution to ecosystem functioning. This is caused by the difficulty to quantify (except in waters), classify (due to their diversity), and to assemble phage genomes out of metagenomics reads (again due to their huge genome plasticity). Last but not least, it is difficult to predict which phage infects which bacterial species. In first attempts at sequencing the viral fraction of bacterial ecosystems, it was concluded that more than 80% of the reads could not be interpreted. Recent improvements have opened the door for more promising assembly analyses: (i) the use of co-variance analysis to selectively assemble reads having the same abundance across samples(Duthil BE et al., Nat Com 2014); (ii) data mining of draft bacterial genomes for the presence of putative prophages. The later approach allows the demonstration that tetramer composition of phage genomes could be used to predict their target host(Roux S et al., eLife 2015). Based on such a comprehensive database of phage proteins, a tool allowing annotation of assembled viral sequences out of metagenomics datasets (virSorterRoux S et al., PeerJ 2014) has also been produced. VIROME ACCESS is a project that brings together molecular ecologists and statisticians from INRA to take on the challenges of virome analyses. Food, intestinal and anaerobic digester samples are used as starting materials. The project has four main objectives.
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Dates et versions

hal-01531724 , version 1 (01-06-2017)

Identifiants

  • HAL Id : hal-01531724 , version 1
  • PRODINRA : 384747

Citer

Marianne de Paepe, Eric Dugat-Bony, Jérôme Hamelin, Mahendra Mariadassou, Kim Milferstedt, et al.. Accessing virus genomes out of metagenomic data: improving statistical and bioinformatics analytic tools to better assess the contribution of phages on microbial ecosystems. Phages On Marseille, Nov 2016, Marseille, France. pp.1. ⟨hal-01531724⟩
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