Comparative genome analysis of Clostridium beijerinckii strains isolated from pit mud of Chinese strong flavor baijiu ecosystem

Abstract

Clostridium beijerinckii is a well-known anaerobic solventogenic bacterium which inhabits a wide range of different niches. Previously, we isolated five butyrate-producing C. beijerinckii strains from pit mud (PM) of strong-flavor baijiu (SFB) ecosystems. Genome annotation of the five strains showed that they could assimilate various carbon sources as well as ammonium to produce acetate, butyrate, lactate, hydrogen, and esters but did not produce the undesirable flavours isopropanol and acetone, making them useful for further exploration in SFB production. Our analysis of the genomes of an additional 233 C. beijerinckii strains revealed an open pangenome based on current sampling and will likely change with additional genomes. The core genome, accessory genome, and strain-specific genes comprised 1567, 8851, and 2154 genes, respectively. A total of 298 genes were found only in the five C. beijerinckii strains from PM, among which only 77 genes were assigned to Clusters of Orthologous Genes (COG) categories. In addition, 15 transposase and 12 phage integrase families were found in all five C. beijerinckii strains from PM. Between 18 and 21 genome islands (GIs) were predicted for the five C. beijerinckii genomes. The existence of a large number of MGEs indicated that the genomes of the five C. beijerinckii strains evolved with the loss or insertion of DNA fragments in the PM of SFB ecosystems. This study presents a genomic framework of C. beijerinckii strains from PM that could be used for genetic diversification studies and further exploration of these strains.

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 ).…”

Phylogenomics and genetic analysis of solvent-producing Clostridium species

“…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 .…”

Solvent-Producing Clostridia Revisited

“…In the other investigation undertaken by Zou et al [ 36 ], the genomes of five newly isolated C. beijerinckii strains from pit mud of strong-flavor baijiu ecosystems were sequenced and added to 233 genomes of other C. beijerinckii strains and used for pangenome analysis. The average genome size of the genomes was 6.11 Mb, and the average number of proteins was 5182.…”