Interactions in the bacterial pathobiome associated with crown gall disease: coexistence or competition?

Our research focuses on various aspects of phytobacteriology. In particular, we deal with the etiology of bacterial diseases of plants, characterization of causative agents, including taxonomy, genetic diversity, genomic features, and evolution of bacteria associated with diseased plants. In addition, we investigate the composition and functions of bacterial communities of diseased plants (i.e., the pathobiome).

The ultimate goal of our research is to contribute to the development of new and more sustainable strategies for disease management. In order to achieve our research objectives, it is often required to perform computationally intensive analyses that cannot be processed easily on personal computers. In 2020, I attended the 6th Joint Conference of DGHM & VAAM, where I noticed the booth of de.NBI and learned about the possibilities this platform offers.

Since then, we use de.NBI cloud for our bioinformatics computations almost on a daily basis. The de.NBI cloud provided us with the easy accessible and scalable working environment which we could freely adapt to serve our research needs. In particular, we used de.NBI virtual machines for de novo assembly of bacterial genomes, functional annotation, core- and pan-genome analyses and phylogenetic inferences. The powerful GPUs of de.NBI were used for basecalling Nanopore DNA sequencing data. Moreover, high-throughput data generated by amplicon sequencing (metabarcoding) approach were also routinely processed. Accordingly, de.NBI computational resources facilitated our numerous studies. When necessary, the de.NBI support team provided us with prompt assistance.

Taken together, de.NBI cloud have proven to be indispensable for our bioinformatics analyses, and enabled planning of new research projects. Therefore, we are planning to use this platform in the future and recommended it to our colleagues.

Nemanja Kuzmanović
Nemanja Kuzmanović from AG Kuzmanovic, Institute of Plant Protection in Horticulture and Urban Green, Julius Kühn Institute (JKI), Braunschweig