Virulent coliphages in 1-year-old children fecal samples are fewer, but more infectious than temperate coliphages

• Published in: Nature communications Vol. 11; no. 1; p. 378
• Main Authors: Mathieu, Aurélie, Dion, Moïra, Deng, Ling, Tremblay, Denise, Moncaut, Elisabeth, Shah, Shiraz A., Stokholm, Jakob, Krogfelt, Karen A., Schjørring, Susanne, Bisgaard, Hans, Nielsen, Dennis S., Moineau, Sylvain, Petit, Marie-Agnès
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 17.01.2020; Nature Publishing Group; Nature Portfolio
• Subjects: 45; 45/22; 45/23; 45/47; 631/326/432; 64; 704/158/855; Carrier Proteins; Children; Coliphages - classification; Coliphages - genetics; Coliphages - isolation & purification; Coliphages - physiology; Dogs; E coli; Escherichia coli - classification; Escherichia coli - isolation & purification; Escherichia coli - virology; Feces; Feces - microbiology; Feces - virology; Gastrointestinal Microbiome; Genome, Viral; Host range; Host Specificity; Humanities and Social Sciences; Humans; Infant; Infants; Infectivity; Intestinal microflora; Life Sciences; Lysogeny; Microbiomes; Microbiota; multidisciplinary; Phages; Science; Science (multidisciplinary); Species Specificity; fewer; children; coliphages
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-019-14042-z

Bacteriophages constitute an important part of the human gut microbiota, but their impact on this community is largely unknown. Here, we cultivate temperate phages produced by 900 E. coli strains isolated from 648 fecal samples from 1-year-old children and obtain coliphages directly from the viral fraction of the same fecal samples. We find that 63% of strains hosted phages, while 24% of the viromes contain phages targeting E. coli . 150 of these phages, half recovered from strain supernatants, half from virome (73% temperate and 27% virulent) were tested for their host range on 75 E. coli strains isolated from the same cohort. Temperate phages barely infected the gut strains, whereas virulent phages killed up to 68% of them. We conclude that in fecal samples from children, temperate coliphages dominate, while virulent ones have greater infectivity and broader host range, likely playing a role in gut microbiota dynamics. The impact of bacteriophages in the human gut microbiome remains poorly understood. Here, the authors characterize coliphages isolated from a large cohort of 1-year-old infants and show that temperate coliphages dominate, while virulent ones have greater infectivity and broader host range.