Phage-based depletion of Variovorax reveals interactions within intact microbiomes

Background Testing microbial interaction hypotheses, including metabolite cross-feeding, remains a major challenge in microbiome research. Phages have the potential to probe organism-organism interactions within complex microbiomes yet are rarely utilised for this purpose. Results Here, we isolated nine narrow host-range phages that replicate in several ecologically important Variovorax species. We used three of the phages to deplete Variovorax SCN45 from complex enrichment communities (containing 18 to 31 species) to test correlation network-based hypothesis of thiamine interdependencies . Genome-resolved metagenomics revealed that a Leifsonia population decreased in relative abundance following Variovorax SCN45 depletion but could be rescued by thiamine supplementation. As a further demonstration of this approach, we used phages to eliminate Variovorax CL14 from a defined rhizosphere co-culture grown with Arabidopsis , where Variovorax CL14 degrades the plant hormone auxin produced by Arthrobacter CL28, and re-established the stunted root phenotype. Conclusion Thus we confirmed thiamine production as the mechanistic basis for interdependence between Variovorax and Leifsonia . These experiments lay the foundation for research that employs wildtype and engineered phages to test interaction hypotheses and for targeted microbiome manipulation.