Journal Article

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

van Passel, Mark W. J., Gutleben, Johanna, Sipkema, Detmer, Gavriilidou, Asimenia, Ingham, Colin J., Smidt, Hauke, Versluis, Dennis, Forgiarini, Francesca

2020

Overview

Background Members of the bacterial family Flavobacteriaceae are 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 family Flavobacteriaceae from 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. Results Comparative 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 marine Flavobacteriaceae to utilize diverse carbon sources. Homologs of gliding proteins were widespread among all studied Flavobacteriaceae in contrast to members of other phyla, highlighting the particular presence of this feature within the Bacteroidetes . Notably, not all bacteria predicted to glide formed spreading colonies. Genome mining uncovered a diverse secondary metabolite biosynthesis arsenal of Flavobacteriaceae with 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. Conclusions Our study elucidates the functional repertoire of marine Flavobacteriaceae and highlights the need to combine genomic and experimental data while using the appropriate stimuli to unlock their uncharted metabolic potential.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Algae / Animal Genetics and Genomics / Animals / Antiinfectives and antibacterials / Antimicrobial activity / Antioxidants / Bacteria / Bacterial motility / Biomedical and Life Sciences / Biosynthesis / Carbohydrate Metabolism / Carbohydrates / Carbon sources / Comparative analysis / Comparative genomics / Cyanobacteria / Cytotoxicity / Detritus / DNA, Bacterial / Ecological niches / Enzymes / Flavobacteriaceae / Flavobacteriaceae - genetics / Free-living / Gene clusters / Genes / Genetic aspects / Genomes / Genomic analysis / Genomics / Gliding / Homology / Host-associated / Invertebrates / Life Sciences / Marine / Marine environment / Marine fish / Marine invertebrates / Metabolism / Metabolites / Methods / Microarrays / Microbial Genetics and Genomics / Microbial metabolism / Motility / Niches / Phenotypes / Phylogenetics / Phylogeny / Physiological aspects / Plant Genetics and Genomics / Polymers / Polysaccharides / Prokaryote microbial genomics / Proteins / Proteomics / Research Article / RNA, Ribosomal, 16S - genetics / rRNA 16S / Sequence Analysis, DNA / Staphylococcus infections / Strains (organisms) / Taxonomy