title: Polymorphism of the phosphoserine phosphatase gene in Streptococcus thermophilus and its potential use for typing and monitoring of population diversity.
abstract: The phosphoserine phosphatase gene (serB) of Streptococcus thermophilus is the most polymorphic gene among those used in Multilocus Sequence Typing schemes for this species and has been used for both genotyping of isolates and for evaluation of population diversity. However, the information on the potential of this gene as a marker for diversity in S. thermophilus species is still fragmentary. In this study, we evaluated serB nucleotide polymorphism and its potential impact on protein structure using data from traditional sequencing. In addition we evaluated the ability of serB targeted high-throughput sequencing in studying the diversity of S. thermophilus populations in cheese and starter cultures. Data based on traditional cultivation based techniques and sequencing provided evidence that the distribution of serB alleles varies significantly in some environments (commercial starter cultures, traditional starter cultures, cheese). Mutations had relatively little impact on predicted protein structure and were not found in domains that are predicted to be important for its functionality. Cultivation independent, serB targeted high-throughput sequencing provided evidence for significantly different alleles distribution in different cheese types and detected fluctuations in alleles abundance in a mixed strain starter reproduced by backslopping. Notwithstanding some shortcomings of this method that are discussed here, the cultivation independent approach appears to be more sensitive than cultivation based approaches based on isolation and traditional sequencing.
authors: Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, Potenza, Italy.
authors: Annamaria
authors: A
authors: Ricciardi
authors: Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Portici, Italy.
authors: Francesca
authors: F
authors: De Filippis
authors: Istituto di Scienze dell'Alimentazione, CNR, Avellino, Italy.
authors: Teresa
authors: T
authors: Zotta
authors: Istituto di Scienze dell'Alimentazione, CNR, Avellino, Italy.
authors: Angelo
authors: A
authors: Facchiano
authors: Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Portici, Italy.
authors: Danilo
authors: D
authors: Ercolini
authors: Dipartimento di Scienze, Università degli Studi della Basilicata, Potenza, Italy. Electronic address: eugenio.parente@unibas.it.
authors: Eugenio
authors: E
authors: Parente
mesh_terms: D000818:Animals; D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D001483:Base Sequence; D044822:Biodiversity; D002417:Cattle; D002611:Cheese / Q000382:microbiology*; D005516:Food Microbiology; D005838:Genotype; D008892:Milk / Q000382:microbiology; D008969:Molecular Sequence Data; D058885:Multilocus Sequence Typing; D010744:Phosphoric Monoester Hydrolases / Q000235:genetics* / Q000378:metabolism; D011110:Polymorphism, Genetic; D048249:Streptococcus thermophilus / Q000145:classification / Q000201:enzymology* / Q000235:genetics / Q000302:isolation & purification
chemical_list: D001426:Bacterial Proteins; D010744:Phosphoric Monoester Hydrolases; C022394:phosphoserine phosphatase
keywords: High-throughput sequencing; Microdiversity; Phosphoserine phosphatase; Streptococcus thermophilus