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

Abstract

Clostridium tyrobutyricum has been recognized as the main cause of late blowing defects (LBD) in cheese leading to considerable economic losses for the dairy industry. Although differences in spoilage ability among strains of this species have been acknowledged, potential links to the genetic diversity and functional traits remain unknown. In the present study, we aimed to investigate and characterize genomic variation, pan-genomic diversity and key traits of C. tyrobutyricum by comparing the genomes of 28 strains. A comparative genomics analysis revealed an “open” pangenome comprising 9,748 genes and a core genome of 1,179 genes shared by all test strains. Among those core genes, the majority of genes encode proteins related to translation, ribosomal structure and biogenesis, energy production and conversion, and amino acid metabolism. A large part of the accessory genome is composed of sets of unique, strain-specific genes ranging from about 5 to more than 980 genes. Furthermore, functional analysis revealed several strain-specific genes related to replication, recombination and repair, cell wall, membrane and envelope biogenesis, and defense mechanisms that might facilitate survival under stressful environmental conditions. Phylogenomic analysis divided strains into two clades: clade I contained human, mud, and silage isolates, whereas clade II comprised cheese and milk isolates. Notably, these two groups of isolates showed differences in certain hypothetical proteins, transcriptional regulators and ABC transporters involved in resistance to oxidative stress. To the best of our knowledge, this is the first study to provide comparative genomics of C. tyrobutyricum strains related to LBD. Importantly, the findings presented in this study highlight the broad genetic diversity of C. tyrobutyricum, which might help us understand the diversity in spoilage potential of C. tyrobutyricum in cheese and provide some clues for further exploring the gene modules responsible for the spoilage ability of this species.

Whole spectrum of Aeromonas hydrophila virulence determinants and the identification of novel SNPs using comparative pathogenomics

“…The valid members of A. hydrophila have been selected for further analysis, and the misidentified strains were excluded. This was based on the threshold value that indicates the presence of the same species of ANI being greater than 94% 22 , 28 . For confirmation of ANI results, the recommended BLAST+ method was utilized to create digital DNA-DNA hybridization (dDDH) values for DNA-DNA hybridization using the Genome-to-Genome Distance Calculator online server (GGDC v3) 29 .…”

“…strains were functionally re-annotated using the Prokka suite, version 1.14.6. The following settings were used to predict the protein-coding genes: -genus Aeromonas -species hydrophila -evalue 1e−09 -coverage 80 -mincontiglen 200) according to Podrzaj et al 28 . Roary 30 was then used to build the core- and pan-genome of Aeromonas spp.…”

“…PanGP 31 tool was used to visualize both the core and pangenomes, by using a gene presence/absence matrix generated from Roary as an input. In brief, pan-genome curve-fitting was achieved using Heaps' law, as described by Podrzaj et al 28 . The curve equation was (y pan = A pan x Bpan + C pan ), where y is the size of the pan-genome, x is the number of genomes, while A, B, and C are the curve-fitting parameters.…”

Clostridium strain FAM25158, a unique endospore-forming bacterium related to Clostridium tyrobutyricum and isolated from Emmental cheese shows low tolerance to salt

“…Although Clostridium species butyricum , sporogenes , and beijerinckii have been associated with LBD ( Klijn et al, 1994 ; Klijn et al, 1995 ; Cocolin et al, 2004 ; Le Bourhis et al, 2007 ; Garde et al, 2011a ; Brändle et al, 2018b ), it is known that Clostridium tyrobutyricum is the main cause of this defect in most cheese types. However, a remarkable degree of phenotypic and genetic diversity has been widely reported among strains of the C. tyrobutyricum species ( Garde et al, 2012 ; Ruusunen et al, 2012 ; Bermudez et al, 2016 ; Burtscher et al, 2020 ; Podrzaj et al, 2020 ; Podrzaj et al, 2022 ).…”

“…In addition, fingerprinting studies demonstrated low similarity of strain FAM25158 to the fingerprints of other C. tyrobutyricum strains ( Burtscher et al, 2020 ). Furthermore, genomic comparison of C. tyrobutyricum strains revealed a distant genetic relationship between strain FAM25158 and 28 C. tyrobutyricum strains ( Podrzaj et al, 2022 ). Therefore, in this study, we aimed to extend the investigation of strain FAM25158 to elucidate its characteristics and assess its significance.…”