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Phages infecting Faecalibacterium prausnitzii belong to novel viral genera that
help to decipher intestinal viromes
#MMPMID29615108
Cornuault JK
; Petit MA
; Mariadassou M
; Benevides L
; Moncaut E
; Langella P
; Sokol H
; De Paepe M
Microbiome
2018[Apr]; 6
(1
): 65
PMID29615108
show ga
BACKGROUND: Viral metagenomic studies have suggested a role for bacteriophages in
intestinal dysbiosis associated with several human diseases. However,
interpretation of viral metagenomic studies is limited by the lack of knowledge
of phages infecting major human gut commensal bacteria, such as Faecalibacterium
prausnitzii, a bacterial symbiont repeatedly found depleted in inflammatory bowel
disease (IBD) patients. In particular, no complete genomes of phages infecting F.
prausnitzii are present in viral databases. METHODS: We identified 18 prophages
in 15 genomes of F. prausnitzii, used comparative genomics to define eight phage
clades, and annotated the genome of the type phage of each clade. For two of the
phages, we studied prophage induction in vitro and in vivo in mice. Finally, we
aligned reads from already published viral metagenomic data onto the newly
identified phages. RESULTS: We show that each phage clade represents a novel
viral genus and that a surprisingly large fraction of them (10 of the 18 phages)
codes for a diversity-generating retroelement, which could contribute to their
adaptation to the digestive tract environment. We obtained either experimental or
in silico evidence of activity for at least one member of each genus. In
addition, four of these phages are either significantly more prevalent or more
abundant in stools of IBD patients than in those of healthy controls. CONCLUSION:
Since IBD patients generally have less F. prausnitzii in their microbiota than
healthy controls, the higher prevalence or abundance of some of its phages may
indicate that they are activated during disease. This in turn suggests that
phages could trigger or aggravate F. prausnitzii depletion in patients. Our
results show that prophage detection in sequenced strains of the microbiota can
usefully complement viral metagenomic studies.
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