Diversity and Evolution of Clostridium beijerinckii and Complete Genome of the Type Strain DSM 791T

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.

Comparative Genomics Provides Insights Into Genetic Diversity of Clostridium tyrobutyricum and Potential Implications for Late Blowing Defects in Cheese

“…Furthermore, the fitted curve for the pangenome profile showed that the fitted exponent of the curve was positive, indicating that the pangenome of C. tyrobutyricum is open. This observation is in agreement with the few published reports on this topic on other members of the genus Clostridium cluster I ( Udaondo et al, 2017 ), such as Clostridium baratii ( Silva-Andrade et al, 2022 ), C. perfringens ( Kiu et al, 2017 ; Feng et al, 2020 ), C. beijerinckii ( Sedlar et al, 2021 ; Zou et al, 2021a ), and C. butyricum ( Zou et al, 2021b ). Open pangenomes may indicate the necessity of constant genomic adaptations and diversification to cope with heterogeneous environments ( Medini et al, 2005 ; Rouli et al, 2015 ).…”

“…Finally, genes with “unknown functions” were enriched in all three pangenome fractions (core, accessory, and strain-specific genes), indicating that there are still many features of C. tyrobutyricum that remain unreported. The over-representation of “function unknown” in the COG categories was similar to what has been observed in other studies of Clostridium species including C. beijerinckii , C. butyricum , and C. ljungdahlii ( Philips et al, 2017 ; Sedlar et al, 2021 ; Zou et al, 2021a ).…”

“…The housekeeping COG categories included “amino acids transport and metabolism” (9.33%) “inorganic ion transport and metabolism” (6.14%), “energy production and conversion” (8.32%), and “coenzyme transport and metabolism” (5.46%). High abundance of these gene categories within the core genome indicates that the strains are metabolically similar, which is consistent with other clostridia, including C. butyricum , C. beijerinckii , C. sporogenes , and C. baratii , which have open pangenomes ( Wu et al, 2017 ; Sedlar et al, 2021 ; Zou et al, 2021b ; Silva-Andrade et al, 2022 ). Furthermore, genes from the category “translation, ribosomal structure and biogenesis” were also abundant in the core genome (1.59%).…”

Phylogenomics and genetic analysis of solvent-producing Clostridium species

“…In an earlier study the genomes of 30 solventogenic Clostridium species from two distinct phylogenetic clades were sequenced 8 , and a phylogenomic analyses of the species was undertaken. A number of misclassified strains were identified that require taxonomic reclassification 39 , which is consistent with the findings of our study.…”

“…Of the genomes sequenced for 194 strains classified as C. beijerinckii this study has clearly established these strains belong to 4 different subgroups or subspecies. The DJ genome sequences generated in this study have already been utilized in 3 recently published phylogenetic and taxonomic studies of solvent producing and C. beijerinckii species 7 , 39 , 42 . The C. beijerinckii genomes have provided a resource for comparison with newly isolated strains for 5 butyrate-producing strains from strong-flavor baijiu ecosystems 42 .…”