RoseXPhLORE: news from the midpoint of the project
NGS-aided exploration of phytopathogenic bacteria diversity in the rose family for sustainable phage-based biocontrol solutions
What the project is about
Rose family plants (Rosaceae) — apples, pears, cherries, plums, apricots, and strawberries — are among the most economically important plant families in the world, and they make up a large share of Latvia’s fruit and berry exports. As the climate warms, bacterial plant diseases are increasingly able to spread and establish themselves, creating a need for new, environmentally friendly ways to control them. One of the most promising alternatives to chemicals and antibiotics is bacteriophages: viruses that selectively infect and destroy specific bacteria while leaving the rest of the plant’s and the environment’s microbiome untouched.
Over three growing seasons (2025–2027), the RoseXPhLORE project is mapping which phytopathogenic bacteria occur on rose family crops grown in Latvia, while simultaneously isolating and characterizing the bacteriophages that infect them — laying the groundwork for the first locally tailored phage-based plant protection products.
What we have achieved at the midpoint
- Material from diseased and healthy rose family plants (apples, pears, cherries, plums, apricots, strawberries) has been collected across almost all Latvian municipalities — 383 samples so far (282 in 2025, 101 in 2026 to date).
- From these samples, 165 distinct bacterial isolates have been isolated, purified, and tentatively identified, representing at least 21 bacterial genera and around 45 species. The most common are Pseudomonas spp. (~61%) and Erwinia spp. (~21%).
- A deep dive was carried out into Erwinia billingiae — a puzzling species usually considered harmless, yet occasionally linked to disease in both plants and, rarely, humans. Using state-of-the-art long-read sequencing, the team assembled 27 complete or near-complete genomes of this bacterium, nearly tripling the number of high-quality E. billingiae genomes publicly available worldwide. The results have been written up in a manuscript submitted to a high-quality journal relevant to the field.
- Around 40 novel bacteriophages infecting rose-family bacterial pathogens have been isolated; 24 of them have already been sequenced and are undergoing careful final manual checks before public release.
- Overall, more genomic data has already been released than promised — 35 bacterial genome assemblies are publicly available at the midpoint, against an initial target of 18 for the entire three-year project.
- Owing to the visibility gained through the project, new international collaboration opportunities have emerged. These include a bilateral mobility project with the Institute of Experimental Botany of the Czech Academy of Sciences funded by the Latvian Academy of Sciences and the Czech Academy of Sciences on plant–bacterium–phage interactions, as well as the participation of several colleagues in the recently approved European COST Action “Phage4Crops”.
- Two University of Latvia biology students have joined the team and have completed coursework and bachelor’s theses on rose-family bacteria and their phages; one PhD student is working on the project.
- The project’s progress has been shared with school pupils and the wider public through shadow days, lab tours at the Biomedical Research and Study Centre, and lectures at a young biologists’ school.
What is still ahead
- Sampling will continue through the end of the 2027 growing season, covering an ever-wider geographical area of Latvia.
- Identification and characterization will continue for the hundreds of bacterial isolates already collected but not yet processed.
- Sequencing and functional annotation of the newly isolated bacteriophage genomes will be completed, along with careful quality control and submission to international public biological sequence repositories.
- The host range of each phage — which bacterial species and strains it can infect — will be investigated, working toward the first hypothetical prototype of a local phage “cocktail” as an eco-friendly plant protection tool.
- Laboratory protocols for whole-genome sequencing of bacteria and bacteriophages will continue to be optimized to further reduce the cost per sample.
- International scientific collaboration will continue, together with the preparation of new scientific publications and research project proposals.
- At the conclusion of the project, a public outreach event is planned to present and summarize all results achieved during the project.
Figure 1. Sampling locations for the Rose family plant material that was utilized for the isolation of both bacterial isolates and their corresponding bacteriophages. For this visualization, Latvia is divided into 43 administrative units (36 municipalities and 7 state cities) to which the sampling locations are mapped. Year 2026 sampling is ongoing, and currently shown up to the middle of June only.
RoseXPhLORE: NGS-Aided Exploration of Phytopathogenic Bacteria Diversity in the Rose Family for Sustainable Phage-Based Biocontrol Solutions (RoseXPhLORE) (project No. lzp-2024/1-0080) is carried out by the National Institute of Research and Innovation in cooperation with the Institute of Horticulture, and is funded by the Latvian Council of Science.
Information published 05.08.2026