Draft Genome Sequence of Clostridium estertheticum subsp. laramiense DSM 14864 T , Isolated from Spoiled Uncooked Beef

et al. 2020

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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.

Section: Introductionmentioning

confidence: 99%

Comparative genomics ofClostridiumspecies associated with vacuum-packed meat spoilage

et al. 2020

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“…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.…”

Section: Announcementmentioning

confidence: 99%

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

Microbiol Resour Announc

Carvalho

et al. 2021

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Here, we present a 16S rRNA gene amplicon sequence data set and profiles demonstrating the bacterial diversity of larval and adult Lucilia sericata, collected from Ashhurst, New Zealand (May 2020). The two dominant genera among adult male and female L. sericata were Serratia and Morganella (phylum Proteobacteria), while the larvae were also dominated by the genera Lactobacillus, Carnobacterium, and Lactococcus (phylum Firmicutes).

“…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.…”

Section: Announcementmentioning

confidence: 99%

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

Carvalho

et al. 2021

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Here, we present a 16S rRNA gene amplicon sequence data set and profiles demonstrating the bacterial diversity of larval and adult Calliphora vicina, collected from Ashhurst, New Zealand (May 2020). The three dominant genera among adult male and female C. vicina were Serratia and Morganella (phylum Proteobacteria) and Carnobacterium (phylum Firmicutes), while the larvae were also dominated by the genera Lactobacillus (phylum Firmicutes).