First Complete Genome Sequence of Staphylococcus xylosus, a Meat Starter Culture and a Host to Propagate Staphylococcus aureus Phages.
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ABSTRACT:
SUBMITTER: Labrie SJ
PROVIDER: S-EPMC4110768 | biostudies-literature | 2014 Jul
REPOSITORIES: biostudies-literature
Publications
First Complete Genome Sequence of Staphylococcus xylosus, a Meat Starter Culture and a Host to Propagate Staphylococcus aureus Phages.
Labrie Simon J SJ El Haddad Lynn L Tremblay Denise M DM Plante Pier-Luc PL Wasserscheid Jessica J Dumaresq Jeannot J Dewar Ken K Corbeil Jacques J Moineau Sylvain S
Genome announcements 20140710 4
Staphylococcus xylosus is a bacterial species used in meat fermentation and a commensal microorganism found on animals. We present the first complete circular genome from this species. The genome is composed of 2,757,557 bp, with a G+C content of 32.9%, and contains 2,514 genes and 79 structural RNAs. ...[more]
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Project description:Team1 (vB_SauM_Team1) is a polyvalent staphylococcal phage belonging to the Myoviridae family. Phage Team1 was propagated on a Staphylococcus aureus strain and a non-pathogenic Staphylococcus xylosus strain used in industrial meat fermentation. The two Team1 preparations were compared with respect to their microbiological and genomic properties. The burst sizes, latent periods, and host ranges of the two derivatives were identical as were their genome sequences. Phage Team1 has 140,903 bp of double stranded DNA encoding for 217 open reading frames and 4 tRNAs. Comparative genomic analysis revealed similarities to staphylococcal phages ISP (97%) and G1 (97%). The host range of Team1 was compared to the well-known polyvalent staphylococcal phages phi812 and K using a panel of 57 S. aureus strains collected from various sources. These bacterial strains were found to represent 18 sequence types (MLST) and 14 clonal complexes (eBURST). Altogether, the three phages propagated on S. xylosus lysed 52 out of 57 distinct strains of S. aureus. The identification of phage-insensitive strains underlines the importance of designing phage cocktails with broadly varying and overlapping host ranges. Taken altogether, our study suggests that some staphylococcal phages can be propagated on food-grade bacteria for biocontrol and safety purposes.
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Project description:Staphylococcus xylosus is used as starter culture for sausage fermentation for a long time but the molecular mechanisms for its adaptation in meat remained unknown. A global transcriptomic approach was carried out to determine these molecular mechanisms. S. xylosus modulated the expression of about 30% of the total genes during its growth and survival in the meat model. The expression of many genes encoding enzymes involved in glucose and lactate catabolism was up regulated. In parallel, genes encoding transport of peptides and peptidases that could furnish amino acids were up expressed and thus concomitantly a lot of genes involved in amino acids synthesis were down regulated. Finally S. xylosus responded to salt added in the meat model by over expressing genes involved in transport and synthesis of osmoprotectants, Na+ and H+ extrusion and in production of energy through the F0F1-ATPase.
2016-01-04 | GSE69743 | GEO
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2016-01-04 | E-GEOD-69743 | biostudies-arrayexpress
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Project description:BackgroundViruses that infect bacteria, called phages, are well-known for their extreme mosaicism, in which an individual genome shares many different parts with many others. The mechanisms for creating these mosaics are largely unknown but are believed to be recombinations, either illegitimate, or partly homologous. In order to reconstruct the history of these recombinations, we need to identify the positions where recombinations may have occurred, and develop algorithms to generate and explore the possible reconstructions.ResultsWe first show that, provided that their gene order is co-linear, genomes of phages can be aligned, even if large parts of their sequences lack any detectable similarity and are annotated hypothetical proteins. We give such an alignment for 31 Staphylococcus aureus phage genomes, and algorithms that can be used in any similar context. These alignments provide the datasets needed for a combinatorial study of recombinations. We next reconstruct the most likely recombination history of the set of 31 phages, under the hypothesis that recombinations are partly homologous. This history relies on the computational identification of missing phages.ConclusionsThis first combinatorial study of modular recombinations acts as a proof of concept. We show that alignments of whole genomes are feasible for large sets of phages, and that this representation yields data that can be used to reconstruct parts of the evolutionary history of these organisms.
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