PhageOS – Prophage-Encoded Functional Reprogramming of Veillonella atypica’s Commensal-to-Accessory Pathogen Transition in the Oral Microbiome in Relation to Periodontitis

Periodontitis is a chronic inflammatory disease linked to systemic health problems, arising from microbial dysbiosis and imbalanced immune response in the oral cavity. The oral microbiome continually adapts to internal and external changes through horizontal gene transfer, with phage-mediated transduction being one of major mechanisms that can supply bacteria with new genes, altering their functional roles. Notably, Veillonella atypica, generally beneficial oral bacteria, may adapt an accessory pathogen role during periodontitis, though the drivers of its functional shift remain unclear. The goal of this project is to determine how prophage-encoded genes influence V. atypica’s transformation from a commensal to a dysbiotic biofilm-supporting accessory periopathogen. To address this, we will perform comparative genomics analysis across V. atypica strains from plaque and saliva samples from periodontitis patients and healthy controls. We will further examine prophage gene activation under oxidative stress using bulk and single-cell SLAM-seq. Finally, we will test biofilm behavior of selected V. atypica strains under oxidative stress and baseline conditions. Findings of this project will be disseminated through two open-access scientific manuscripts, two presentations at leading international conferences, multiple dataset deposition into public repositories, as well as through activities, aimed at the broader public.

Planned results

• Original research articles published in the Q1 or Q2 publications listed in the Web of Science or SCOPUS databases – 2
• Other peer-reviewed original research articles in other scientific journals and collections of articles (including conference article collections), with an international editorial board – 2
• Scientific databases and datasets prepared according to the FAIR principles – 4
• Other new product or technology, software copyrights (including methods, prototypes, treatment and diagnostic methods not to be commercialised, etc.) – 1
• Project proposal submitted in an international call for research and development projects (competition abroad or submitted by an international consortium) – 1
• Project proposal submitted in a Latvian call for research and development projects – 1
• Other project results according to the specific nature of the project complementary to those listed above (including pre-prints) – 2 preprints

Progress reports 

1st quarter (1 January–31 March 2026)

During the first quarter of the project, the practical implementation of PhageOS was launched and the clinical research component was prepared. The necessary study documentation was developed, and ethics committee approval was obtained for the collection of biological samples. Participant recruitment was initiated in collaboration with the RSU Institute of Stomatology.

At the same time, procedures for sample collection, transportation and laboratory processing were established, and methods for isolating Veillonella atypica from samples and culturing the bacteria under laboratory conditions were prepared.

2nd quarter (1 April–30 June 2026)

Recruitment of patients with periodontitis and collection of biological samples continued in collaboration with the RSU Institute of Stomatology. Saliva and dental plaque samples were collected. With the involvement of the RSU Phage Research Group, V. atypica bacterial cultures were isolated from these samples for further genetic analysis.

Genetic analysis of V. atypica isolated from samples obtained from patients with periodontitis was initiated. The aim is to characterise the genetic composition of the bacteria and identify differences between the patient and control groups. Attention is being paid to prophages – viral genetic material integrated into the bacterial genome – to investigate their potential role in altering bacterial characteristics.

In parallel, Prof. Bhupesh Prusty’s research group continued to refine methods for studying V. atypica RNA. These methods will subsequently make it possible to determine which bacterial genes become active under specific conditions, including the activity of prophage genes.

3rd quarter (1 July–30 September 2026)

Genetic analysis of V. atypica bacteria obtained from the patient group was completed, and in-depth analysis of the resulting data was initiated in collaboration with the RSU Phage Research Group. The genetic characteristics of the bacteria and the potential role of prophages in their changes are being investigated. The first preliminary results have been obtained, providing a basis for the preparation of the project’s first scientific publication and for planning further data analysis. At the same time, recruitment of participants for the control group and collection of biological samples are continuing.

Prof. Prusty’s research group continues to refine methods for studying V. atypica RNA and determining which genes become active in the bacteria and under what conditions. This is necessary to investigate prophage gene activity and its potential role in the transition of V. atypica from a normal member of the oral microbiome to a bacterium that may contribute to disease progression under periodontitis-associated conditions. 

Scientific Team

• Alisa Kazarina – lead researcher, principal investigator
• Bhupesh Kumar Prusty – lead researcher
• Kārlis Rācenis – lead researcher