DOI 10.1016/j.ijfoodmicro.2021.109326 Serratia sp. cause food losses and waste due to spoilage; it is noteworthy that they represent a dominant population in seafood. The main spoilage associated species comprise S. liquefaciens, S. grimesii, S. proteamaculans and S. quinivorans, also known as S. liquefaciens-like strains. These species are difficult to discriminate since classical 16S rRNA gene-based sequences do not possess sufficient resolution. In this study, a phylogeny based on the short-length luxS gene was able to speciate 47 Serratia isolates from seafood, with S. proteamaculans being the main species from fresh salmon and tuna, cold-smoked salmon, and cooked shrimp while S. liquefaciens was only found in cold-smoked salmon.
The genome of the first S. proteamaculans strain isolated from the seafood matrix (CD3406 strain) was sequenced. Pangenome analyses of S. proteamaculans and S. liquefaciens indicated high adaptation potential. Biosynthetic pathways involved in antimicrobial compounds production and in the main seafood spoilage compounds were also identified. The genetic equipment highlighted in this study contributed to gain further insights into the predominance of Serratia in seafood products and their capacity to spoil.
Serratia, Genome mining, Pangenome, Phylogeny, luxS, Spoilage markers
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Publisher's official version | 10 | 2 Mo | ||
Fig. S1. Multiple sequence alignment of luxS gene from Serratia species and other Enterobacteriaceae. Primers uniLuxS-SER_F and ... | 10 | 794 Ko | ||
Fig. S2. Partial 16S rRNA phylogenetic tree. The first 800 bp were aligned with MUSCLE and the tree was obtained with MEGAX ... | 1 | 557 Ko | ||
Fig. S3. 16S rRNA phylogenetic tree. Complete sequences (1554 bp) were aligned with MUSCLE and the tree was obtained with MEGAX ... | 1 | 555 Ko | ||
Fig. S4. atpD phylogenetic tree. DNA sequences were aligned with MUSCLE and the tree was constructed using maximum likelihood ... | 1 | 529 Ko | ||
Fig. S5. gyrB phylogenetic tree. DNA sequences were aligned with MUSCLE and the tree was constructed using maximum likelihood ... | 1 | 533 Ko | ||
Fig. S6. infB phylogenetic tree. DNA sequences were aligned with MUSCLE and the tree was constructed using maximum likelihood ... | 1 | 534 Ko | ||
Fig. S7. infB phylogenetic tree. DNA sequences were aligned with MUSCLE and the tree was constructed using maximum likelihood .... | 1 | 534 Ko | ||
Fig. S8. Phylogenetic tree based on 373 bp-luxS sequence analyses of Serratia strains isolated from seafood products. Tree was obtained .... | 1 | 213 Ko | ||
Fig. S9. Pangenome (A) and core genome (B) of S. marcescens using Microscope platform. 22 genomes were analyzed: Serratia marcescens WW4, Serratia marcescens W2.3, Serratia marcescens VGH107, ... | 1 | 163 Ko | ||
Table S1. ANI clustering of genomes publicly available. In this study, Cluster I corresponds, to S. quinivorans species; cluster II to S. ... | - | 18 Ko | ||
Table S2. Identification of strains isolated from seafood products by luxS sequence analyses. Genotypes were attributed according to the .... | - | 19 Ko | ||
Table S3. ANI calculated for Serratia genomes used in this study. ANI over 95% were colored in red. | - | 36 Ko | ||
Table S4. CD3406 protein sequences potentially involved in seafood spoilage. | - | 24 Ko | ||
Author's final draft | 65 | 9 Mo |
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