@article{fdi:010086871,
  title = {{P}hage-host prediction using a computational tool coupled with 16{S} r{RNA} gene amplicon sequencing},
  author = {{A}ndrianjakarivony, {H}. {F}. and {B}ettarel, {Y}van and {A}rmougom, {F}abrice and {D}esnues, {C}.},
  editor = {},
  language = {{ENG}},
  abstract = {{M}etagenomics studies have revealed tremendous viral diversity in aquatic environments. {Y}et, while the genomic data they have provided is extensive, it is unannotated. {F}or example, most phage sequences lack accurate information about their bacterial host, which prevents reliable phage identification and the investigation of phage-host interactions. {T}his study aimed to take this knowledge further, using a viral metagenomic framework to decipher the composition and diversity of phage communities and to predict their bacterial hosts. {T}o this end, we used water and sediment samples collected from seven sites with varying contamination levels in the {E}brie {L}agoon in {A}bidjan, {I}vory {C}oast. {T}he bacterial communities were characterized using the 16{S} r{RNA} metabarcoding approach, and a framework was developed to investigate the virome datasets that: (1) identified phage contigs with {V}ir{S}orter and {VIBRANT}; (2) classified these contigs with {M}eta{P}hinder using the phage database (taxonomic annotation); and (3) predicted the phages' bacterial hosts with a machine learning-based tool: the {P}rokaryotic {V}irus-{H}ost {P}redictor. {T}he findings showed that the taxonomic profiles of phages and bacteria were specific to sediment or water samples. {P}hage sequences assigned to the {M}icroviridae family were widespread in sediment samples, whereas phage sequences assigned to the {S}iphoviridae, {M}yoviridae and {P}odoviridae families were predominant in water samples. {I}n terms of bacterial communities, the phyla {L}atescibacteria, {Z}ixibacteria, {B}acteroidetes, {A}cidobacteria, {C}alditrichaeota, {G}emmatimonadetes, {C}yanobacteria and {P}atescibacteria were most widespread in sediment samples, while the phyla {E}psilonbacteraeota, {T}enericutes, {M}argulisbacteria, {P}roteobacteria, {A}ctinobacteria, {P}lanctomycetes and {M}arinimicrobia were most prevalent in water samples. {S}ignificantly, the relative abundance of bacterial communities (at major phylum level) estimated by 16{S} r{RNA} metabarcoding and phage-host prediction were significantly similar. {T}hese results demonstrate the reliability of this novel approach for predicting the bacterial hosts of phages from shotgun metagenomic sequencing data.},
  keywords = {virome ; phage-host interaction ; 16{S} r{RNA} metabarcoding ; host prediction ; bacteria ; metagenomic ; lagoon ; {COTE} {D}'{IVOIRE} ; {ABIDJAN} ; {EBRIE} {LAGUNE}},
  booktitle = {},
  journal = {{V}iruses},
  volume = {15},
  numero = {1},
  pages = {76 [12 ]},
  year = {2023},
  DOI = {10.3390/v15010076},
  URL = {https://www.documentation.ird.fr/hor/fdi:010086871},
}