Comparative genomics ofClostridiumspecies associated with vacuum-packed meat spoilage

Abstract

Bacterial species belonging to the Clostridium genera have been recognized as causative agents of blown pack spoilage (BPS) in vacuum packed meat products. Whole-genome sequencing of six New Zealand psychrotolerant Clostridium isolates derived from three meat production animal types and their environments was performed to examine their roles in BPS. Comparative genome analyses have provided insight into the genomic diversity and physiology of these bacteria and divides Clostridia into two separate species clusters. BPS-associated Clostridia encode a large and diverse spectrum of degradative carbohydrate-active enzymes (CAZymes). In total, 516 glycoside hydrolases (GHs), 93 carbohydrate esterases (CEs), 21 polysaccharide lyases (PLs), 434 glycosyl transferases (GTs) and 211 carbohydrate-binding protein modules (CBM) with predicted activities involved in the breakdown and transport of carbohydrates were identified. Clostridia genomes have different patterns of CAZyme families and vary greatly in the number of genes within each CAZy category, suggesting some level of functional redundancy. These results suggest that BPS-associated Clostridia occupy similar environmental niches but apply different carbohydrate metabolism strategies to be able to co-exist and cause meat spoilage.

Whole Genome Sequence-Based Identification of Clostridium estertheticum Complex Strains Supports the Need for Taxonomic Reclassification Within the Species Clostridium estertheticum

“…In the present study, we broadened the analysis to encompass 34 CEC genomes, including five reference strains whose genomes were lacking. Similar to the previous study ( Palevich et al, 2021 ), the 96% ANI was sufficient to delineate all CEC species apart from C. estertheticum . Comparatively, the 70% dDDH for intraspecies delineation ( Meier-Kolthoff et al, 2013 ) also sufficed for all genomospecies apart from C. estertheticum .…”

“…Comparative studies between ANI and DDH values show that ANI values of 95–96% are equivalent to the 70% DDH ( Goris et al, 2007 ; Richter and Rosselló-Móra, 2009 ). In this regard, a recent study used ANI of 96% to delineate six strains into distinct CEC species and showed the value was sufficient ( Palevich et al, 2021 ). In the present study, we broadened the analysis to encompass 34 CEC genomes, including five reference strains whose genomes were lacking.…”

“…Even though, C. frigoriphilum is not a validly published species, it is considered a species within the CEC ( Pecheritsyna et al, 2007 ; Dorn-In et al, 2018 ). Two unnamed novel species within the CEC have also been proposed from recent studies ( Brightwell and Horváth, 2018 ; Palevich et al, 2021 ). The majority of the CEC species have been linked with BPS or other types of meat spoilage ( Húngaro et al, 2016 ).…”

“…Within the CEC, WGS-based analyses have so far been used in very few studies ( Wambui et al, 2020d ; Palevich et al, 2021 ). Furthermore, six species within the CEC lack published genomes hence the taxonomy of CEC beyond 16S rRNA-based classification is not fully known.…”

16S rRNA Gene Amplicon Profiling of the New Zealand parasitic blowflyCalliphora vicina

“…Genomic DNA for metagenomic 16S rRNA gene amplicon sequencing of the V3-V4 hypervariable region was isolated from C. vicina pooled samples of 100 larvae as well as 10 entire adult males and females per replicate ( n =5 for each). High molecular weight genomic DNA was prepared using a modified phenol:chloroform protocol recently applied to difficult samples such as parasitic roundworms (7, 8), fastidious anaerobic rumen bacteria (9–11) and spore-forming psychrotolerant Clostridium isolated from spoiled meat (12, 13). A DNA library was prepared using the Illumina 16S V3-V4 rRNA library preparation method (Illumina, Inc., San Diego, CA) according to the manufacturer’s instructions (20), and sequenced on the Illumina MiSeq platform with the 2× 250 bp paired-end (PE) reagent kit v2 producing a total of 3,017,007 PE raw reads.…”