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

Aurélie Mathieu,Hans Bisgaard,Ling Deng,Sylvain Moineau,Elisabeth Moncaut,Denise Tremblay,Dennis S Nielsen,Shiraz A Shah,Marie-Agnès Petit,Jakob Stokholm,Susanne Schjørring,Moïra Dion,Karen A Krogfelt

doi:10.1038/s41467-019-14042-z

Abstract

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.

Highlights

Bacteriophages constitute an important part of the human gut microbiota, but their impact on this community is largely unknown
We show that temperate phages outnumber virulent ones in fecal samples, and that most E. coli strains isolated from the same cohort are resistant to temperate phages but sensitive to virulent phages
During the first (Fig. 1, left side), we analyzed the temperate phages hosted in 900 E. coli strains previously isolated from these same fecal samples (0–5 isolates per sample, see23)

Summary

Introduction

Bacteriophages constitute an important part of the human gut microbiota, but their impact on this community is largely unknown. A similar study conducted approximately 20 years later examined the fecal samples of 140 Bengal children with acute gastro-enteritis and the authors succeeded in isolating coliphages from 27% of the samples, and 95% of them were virulent[16] These findings support the view that a diarrheal context correlates with virulent phage development. A reanalysis of this dataset focusing on the temperate phages associated with Faecalibacterium prausnitzii, a dominant bacterial member of the human microbiota which is depleted in Crohn’s disease patients, suggested a negative correlation between bacterial and viral abundances for this species[18]. Such a situation may originate from massive prophage induction in a dysbiotic context. This study generates a contrasting picture, where temperate coliphages are relatively abundant but remarkably innocuous to bacteria found in one-year-old children, and virulent phages are sub-dominant but may kill their host upon encounter

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