Novel Siphoviridae Bacteriophages Infecting Bacteroides uniformis Contain Diversity Generating Retroelement

Abstract

Intestinal phages are abundant and important components of gut microbiota, yet the isolated and characterized representatives that infect abundant gut bacteria are sparse. Here we describe the isolation of human intestinal phages infecting Bacteroidesuniformis. Bacteroides is one of the most common bacterial groups in the global human gut microbiota; however, to date not many Bacteroides specific phages are known. Phages isolated in this study belong to a novel viral genus, Bacuni, within the Siphoviridae family. Their genomes encode diversity-generating retroelements (DGR), which were shown in other bacteriophages to promote phage adaptation to rapidly changing environmental conditions and to broaden their host range. Three isolated phages showed 99.83% genome identity but one of them infected a distinct B. uniformis strain. The tropism of Bacuni phages appeared to be dependent on the interplay of DGR mediated sequence variations of gene encoding putative phage fimbrial tip proteins and mutations in host genes coding for outer-membrane proteins. We found prophages with up to 85% amino acid similarity over two-thirds of the Bacuni phage genome in the B. acidifaciens and Prevotella sp. genomes. Despite the abundance of Bacteroides within the human microbiome, we found Bacuni phages only in a limited subset of published gut metagenomes.

Broad host range may be a key to long-term persistence of bacteriophages infecting intestinal Bacteroidaceae species

“…4 e,f). Such opaque zones were noted before for Bacuni phages 19 (cluster C1) and ΦcrAss002 14 . While failing to form plaques or clearings in spot assays, ΦcrAss002 was stably maintained in liquid culture and did not cause any clearing of the host bacteria 14 .…”

“…3 b and 4 ). The importance of host range adaptation was also implied by C5 and C7 phages that carry DGRs, which use reverse transcription to introduce nucleotide substitutions into specific target genes that may mediate host range adaptations 15 , 19 . Notably, most SNPs in C7 phages were found in the DGR target, the predicted phage receptor gene 19 , which is a remote homologue of Bacteroides fimbrial tip protein gene that may have been recruited by C7 phages long time ago 29 .…”

“…Additionally, the following phages that infect Bacteroidaceae species have been isolated and sequenced: two phage clusters that infect B. thetaiotaomicron 13 , B40-8 16 and B124-14 17 that infect Bacteroides fragilis , ϕBrb01 and ϕBrb02 isolated from rumen fluid infecting ruminal Bacteroides sp. 18 and Bacuni phages with DGRs that infect Bacteroides uniformis , recently isolated by our group 19 .…”

Complete Genome Sequences of Two Bacteroides uniformis Bacteriophages

“…In this work, we sought to isolate and characterize phages for Bacteroides uniformis , which may have beneficial metabolic effects ( 5 – 7 ), as tools to study host-phage interactions in the human gut. Thus far, very few phages that infect B. uniformis have been isolated ( 8 , 9 ).…”

Editorial for the Special Issue: The Role of the Virome in Health and Disease

“…These authors also highlight the potential of phage intake to ameliorate some of the symptoms associated with such diseases. Staying in the realm of phages, Hedžet et al report the discovery of Bacteroides-infecting phages from the human intestine that contain a diversity-generating retroelement (DGR) [16]. First identified in Bordetella phage BPP-1, DGRs appear to be evolutionarily co-opted by some phages to generate variation in the proteins required for the infection of the host bacteria, thereby altering or extending the phage's tropism [17].…”