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Phage-Host Prediction Using a Computational Tool Coupled with 16S rRNA Gene Amplicon Sequencing.

Harilanto Felana Andrianjakarivony1,2, Yvan Bettarel3, Fabrice Armougom2

  • 1Microbes, Evolution, Phylogeny, and Infection (MEΦI), IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France.

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Summary

This study developed a new metagenomic framework to identify phage sequences and predict their bacterial hosts in aquatic environments. The findings show distinct phage and bacterial community compositions in water and sediment, validating the predictive approach.

Keywords:
16S rRNA metabarcodingbacteriahost predictionlagoonmetagenomicphage-host interactionvirome

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Area of Science:

  • Environmental metagenomics
  • Virome analysis
  • Microbial ecology

Background:

  • Metagenomics reveals vast viral diversity in aquatic ecosystems, but genomic data remains largely unannotated.
  • Lack of accurate phage-host information hinders phage identification and interaction studies.
  • Aquatic environments like Ebrié Lagoon harbor complex phage communities.

Purpose of the Study:

  • To develop and apply a viral metagenomic framework for deciphering phage community composition and diversity.
  • To predict bacterial hosts for identified phages using a machine learning-based tool.
  • To investigate phage-host interactions in relation to environmental factors (water vs. sediment).

Main Methods:

  • Collected water and sediment samples from Ebrié Lagoon, Ivory Coast.
  • Characterized bacterial communities using 16S rRNA metabarcoding.
  • Analyzed virome datasets using VirSorter, VIBRANT, MetaPhinder, and Prokaryotic Virus-Host Predictor for phage identification, taxonomic annotation, and host prediction.

Main Results:

  • Distinct taxonomic profiles of phages and bacteria were observed between water and sediment samples.
  • Specific phage families (Microviridae in sediment; Siphoviridae, Myoviridae, Podoviridae in water) showed varied distribution.
  • Predicted bacterial phyla distributions showed significant similarity to those identified by 16S rRNA metabarcoding, confirming the approach's reliability.

Conclusions:

  • The developed metagenomic framework reliably identifies phage contigs and predicts their bacterial hosts.
  • Phage and bacterial community structures are site-specific (water vs. sediment) within the Ebrié Lagoon.
  • This approach advances the understanding of phage-host dynamics in aquatic microbial ecosystems.