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Hundreds of viral families in the healthy infant gut

Authors :
Yichang Zhang
Fie Olsen Romme
Marie-Agnès Petit
Sylvain Moineau
Ronalds Silins
Anders Pedersen
Gisle Vestergaard
Dennis Sandris Nielsen
Jonathan Thorsen
Ling Deng
Romain Sausset
François Enault
Josué L. Castro-Mejía
Moïra B. Dion
Shiraz A. Shah
Morten Arendt Rasmussen
Mathis Hjemlsø
Hans Bisgaard
Jakob Stokholm
Eric Olo Ndela
Søren J. Sørensen
Tamsin Redgwell
Publication Year :
2021
Publisher :
Cold Spring Harbor Laboratory, 2021.

Abstract

The gut microbiome (GM) is shaped through infancy and plays a major role in determining susceptibility to chronic inflammatory diseases later in life. Bacteriophages (phages) are known to modulate bacterial populations in numerous ecosystems, including the gut. However, virome data is difficult to analyse because it mostly consists of unknown viruses, i.e. viral dark matter. Here, we manually resolved the viral dark matter in the largest human virome study published to date. Fecal viromes from a cohort of 647 infants at 1 year of age were deeply sequenced and analysed through successive rounds of clustering and curation. We uncovered more than ten thousand viral species distributed over 248 viral families falling within 17 viral order-level clades. Most of the defined viral families and orders were novel and belonged to the Caudoviricetes viral class. Bacterial hosts were predicted for 79% of the viral species using CRISPR spacers, including those in metagenomes from the same fecal samples. While Bacteroides-infecting Crassphages were present, novel viral families were more predominant, including phages infecting Clostridiales and Bifidobacterium. Phage lifestyles were determined for more than three thousand caudoviral species. Lifestyles were homogeneous at the family level for 149 Caudoviricetes families, including 32 families that were found to be virulent, while 117 were temperate. Virulent phage families were more abundant but temperate ones were more diverse and widespread. Together, the viral families found in this study represent a major expansion of existing bacteriophage taxonomy.

Details

Database :
OpenAIRE
Accession number :
edsair.doi...........e631a8eaf0a9ea3a677691b1f9c89be5
Full Text :
https://doi.org/10.1101/2021.07.02.450849