Comparative genomic analysis of Flavobacteriaceae: insights into carbohydrate metabolism, gliding motility and secondary metabolite biosynthesis

• DOI: 10.1186/s12864-020-06971-7
• Publication Date: 2020-08-20T11:02:57Z
• Authors: Asimenia Gavriilidou; Johanna Gutleben; Dennis Versluis; Francesca Forgiarini; Mark W. J. van Pa...; Colin J. Ingham; Hauke Smidt; Detmer Sipkema
• Keywords: DNA, Bacterial; 0301 basic medicine; QH426-470; 03 medical and health sciences; Host-associated; RNA, Ribosomal, 16S; Genetics; Animals; 14. Life underwater; Phylogeny; 0303 health sciences; Marine; Comparative genomics; Genomics; Sequence Analysis, DNA; 15. Life on land; Free-living; Carbohydrate Metabolism; Flavobacteriaceae; TP248.13-248.65; Biotechnology; Research Article

AbstractBackgroundMembers of the bacterial familyFlavobacteriaceaeare widely distributed in the marine environment and often found associated with algae, fish, detritus or marine invertebrates. Yet, little is known about the characteristics that drive their ubiquity in diverse ecological niches. Here, we provide an overview of functional traits common to taxonomically diverse members of the familyFlavobacteriaceaefrom different environmental sources, with a focus on the Marine clade. We include seven newly sequenced marine sponge-derived strains that were also tested for gliding motility and antimicrobial activity.ResultsComparative genomics revealed that genome similarities appeared to be correlated to 16S rRNA gene- and genome-based phylogeny, while differences were mostly associated with nutrient acquisition, such as carbohydrate metabolism and gliding motility. The high frequency and diversity of genes encoding polymer-degrading enzymes, often arranged in polysaccharide utilization loci (PULs), support the capacity of marineFlavobacteriaceaeto utilize diverse carbon sources. Homologs of gliding proteins were widespread among all studiedFlavobacteriaceaein contrast to members of other phyla, highlighting the particular presence of this feature within theBacteroidetes. Notably, not all bacteria predicted to glide formed spreading colonies. Genome mining uncovered a diverse secondary metabolite biosynthesis arsenal ofFlavobacteriaceaewith high prevalence of gene clusters encoding pathways for the production of antimicrobial, antioxidant and cytotoxic compounds. Antimicrobial activity tests showed, however, that the phenotype differed from the genome-derived predictions for the seven tested strains.ConclusionsOur study elucidates the functional repertoire of marineFlavobacteriaceaeand highlights the need to combine genomic and experimental data while using the appropriate stimuli to unlock their uncharted metabolic potential.