Comparative genomics of Clostridium species associated with vacuum-packed meat spoilage

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

Bacterial Diversity Profiling of the New Zealand Parasitic Blowfly Lucilia sericata Based on 16S rRNA Gene Amplicon Sequencing

“…Genomic DNA was prepared for metagenomic 16S rRNA gene amplicon sequencing of the V3-V4 hypervariable region using a modified phenol-chloroform protocol recently described for complex samples, such as parasitic roundworms ( 6 , 7 ), fastidious anaerobic rumen bacteria ( 8 – 10 ), and spore-forming psychrotolerant Clostridium sp. isolated from spoiled meat ( 11 , 12 ). A DNA library was prepared using the 16S V3-V4 rRNA library preparation method (Illumina, Inc., San Diego, CA) according to the manufacturer’s instructions ( 13 ) and sequenced on the Illumina MiSeq platform with the 2 × 250-bp paired-end (PE) reagent kit v2, producing a total of 5,208,027 PE raw reads.…”

16S rRNA Gene Amplicon Profiling of the New Zealand Parasitic Blowfly Calliphora vicina

“…To remove surface adherent bacteria from lab-reared C. vicina, pools of larvae and entire adult males and females were separated and washed twice in sterile phosphate-buffered saline (PBS; pH 7.4), snap-frozen in liquid nitrogen, and transferred to 280°C storage prior to DNA extraction. High-molecular-weight genomic DNA 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), using a modified phenol-chloroform protocol recently applied to difficult samples (7)(8)(9)(10)(11)(12)(13). A DNA library was prepared using the Illumina (San Diego, CA) 16S V3 and V4 rRNA library preparation method according to the manufacturer's instructions (14) and sequenced on the Illumina MiSeq platform with the 2 Â 250-bp paired-end (PE) reagent kit v2, producing a total of 3,017,007 PE raw reads.…”