title: Study of Streptococcus thermophilus population on a world-wide and historical collection by a new MLST scheme.
abstract: We analyzed 178 Streptococcus thermophilus strains isolated from diverse products, from around the world, over a 60-year period with a new multilocus sequence typing (MLST) scheme. This collection included isolates from two traditional cheese-making sites with different starter-use practices, in sampling campaigns carried out over a three years period. The nucleotide diversity of the S. thermophilus population was limited, but 116 sequence types (ST) were identified. Phylogenetic analysis of the concatenated sequences of the six housekeeping genes revealed the existence of groups confirmed by eBURST analysis. Deeper analyses performed on 25 strains by CRISPR and whole-genome analysis showed that phylogenies obtained by MLST and whole-genome analysis were in agreement but differed from that inferred by CRISPR analysis. Strains isolated from traditional products could cluster in specific groups indicating their origin, but also be mixed in groups containing industrial starter strains. In the traditional cheese-making sites, we found that S. thermophilus persisted on dairy equipment, but that occasionally added starter strains may become dominant. It underlined the impact of starter use that may reshape S. thermophilus populations including in traditional products. This new MLST scheme thus provides a framework for analyses of S. thermophilus populations and the management of its biodiversity.
authors.affiliation: Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France. Electronic address: christine.delorme@inra.fr.
authors.forename: Christine
authors.initials: C
authors.lastname: Delorme
authors.affiliation: Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Legravet
authors.affiliation: Actilait, 419, route des champs laitiers, F-74 800 La Roche sur Foron, France.
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Jamet
authors.affiliation: Actilait, 419, route des champs laitiers, F-74 800 La Roche sur Foron, France.
authors.forename: Caroline
authors.initials: C
authors.lastname: Hoarau
authors.affiliation: Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
authors.forename: Bolotin
authors.initials: B
authors.lastname: Alexandre
authors.affiliation: Food Safety and Microbial Physiology Laboratory, Dairy Department, Faculty of Agriculture, Mansoura University, Mansoura, Egypt.
authors.forename: Walid M
authors.initials: WM
authors.lastname: El-Sharoud
authors.affiliation: Food Safety and Microbial Physiology Laboratory, Dairy Department, Faculty of Agriculture, Mansoura University, Mansoura, Egypt.
authors.forename: Mohamed S
authors.initials: MS
authors.lastname: Darwish
authors.affiliation: Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Renault
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D005516:Food Microbiology; D058885:Multilocus Sequence Typing; D010802:Phylogeny; D048249:Streptococcus thermophilus / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins
keywords: Genetic variability; HGT; MLST; Streptococci; Traditional cheese