Abstract
Clostridium beijerinckii is a relatively widely studied, yet non-model, bacterium. While 246 genome assemblies of its various strains are available currently, the diversity of the whole species has not been studied, and it has only been analyzed in part for a missing genome of the type strain. Here, we sequenced and assembled the complete genome of the type strain Clostridium beijerinckii DSM 791T, composed of a circular chromosome and a circular megaplasmid, and used it for a comparison with other genomes to evaluate diversity and capture the evolution of the whole species. We found that strains WB53 and HUN142 were misidentified and did not belong to the Clostridium beijerinckii species. Additionally, we filtered possibly misassembled genomes, and we used the remaining 237 high-quality genomes to define the pangenome of the whole species. By its functional annotation, we showed that the core genome contains genes responsible for basic metabolism, while the accessory genome has genes affecting final phenotype that may vary among different strains. We used the core genome to reconstruct the phylogeny of the species and showed its great diversity, which complicates the identification of particular strains, yet hides possibilities to reveal hitherto unreported phenotypic features and processes utilizable in biotechnology.
Highlights
We discovered that the genome of the type strain is composed of a circular chromosome and a circular megaplasmid that carries a complete cluster of genes to produce bacteriocin circularin A, which is unique among C
We used the genome sequence for whole-genome comparisons, and we found out that at least two strains currently assigned as C. beijerinckii, WB53 and HUN142, do not belong to the species
We proved that some of the genome assemblies, e.g., the genome sequence of the strain C. beijerinckii ASCUSBR67, are of lower quality and should be polished before they can be used for comparative analyses
Summary
Clostridium beijerinckii belongs to the group of authentic Clostridium spp., referred to as Cluster I “Sensu stricto” [1]. As a Gram-positive, spore forming, rod shaped anaerobe capable of solventogenesis, C. beijerinckii represents an industrially relevant microorganism. Butanol is produced within either an acetone-butanol-ethanol (ABE) [2] or isopropanol-butanolethanol (IBE) [3] fermentation pathway that covers a bi-phasic process in which acid formation is later followed by the formation of solvents. Both processes do not seem to be closely linked in all strains [4]. Evolutionary and comparative studies of various clostridial strains are required to help reveal hidden aspects of the production of valuable chemicals by microbial cell factories [5]
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