Species Designations Belie Phenotypic and Genotypic Heterogeneity in Oral Streptococci

ABSTRACT Health-associated oral Streptococcus species are promising probiotic candidates to protect against dental caries. Ammonia production through the arginine deiminase system (ADS), which can increase the pH of oral biofilms, and direct antagonism of caries-associated bacterial species are desi...

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Autores principales:	Irina M. Velsko, Brinta Chakraborty, Marcelle M. Nascimento, Robert A. Burne, Vincent P. Richards
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2018
Materias:	Streptococcus genomics oral microbiology phylogenetic analysis variable phenotypes Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/35f1bfbe8ca34df49f391dccf3ff60ec
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spelling	oai:doaj.org-article:35f1bfbe8ca34df49f391dccf3ff60ec2021-12-02T19:47:34ZSpecies Designations Belie Phenotypic and Genotypic Heterogeneity in Oral Streptococci10.1128/mSystems.00158-182379-5077https://doaj.org/article/35f1bfbe8ca34df49f391dccf3ff60ec2018-10-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00158-18https://doaj.org/toc/2379-5077ABSTRACT Health-associated oral Streptococcus species are promising probiotic candidates to protect against dental caries. Ammonia production through the arginine deiminase system (ADS), which can increase the pH of oral biofilms, and direct antagonism of caries-associated bacterial species are desirable properties for oral probiotic strains. ADS and antagonistic activities can vary dramatically among individuals, but the genetic basis for these differences is unknown. We sequenced whole genomes of a diverse set of clinical oral Streptococcus isolates and examined the genetic basis of variability in ADS and antagonistic activities. A total of 113 isolates were included and represented 10 species: Streptococcus australis, A12-like, S. cristatus, S. gordonii, S. intermedius, S. mitis, S. oralis including S. oralis subsp. dentisani, S. parasanguinis, S. salivarius, and S. sanguinis. Mean ADS activity and antagonism on Streptococcus mutans UA159 were measured for each isolate, and each isolate was whole genome shotgun sequenced on an Illumina MiSeq. Phylogenies were built of genes known to be involved in ADS activity and antagonism. Several approaches to correlate the pan-genome with phenotypes were performed. Phylogenies of genes previously identified in ADS activity and antagonism grouped isolates by species, but not by phenotype. A genome-wide association study (GWAS) identified additional genes potentially involved in ADS activity or antagonism across all the isolates we sequenced as well as within several species. Phenotypic heterogeneity in oral streptococci is not necessarily reflected by genotype and is not species specific. Probiotic strains must be carefully selected based on characterization of each strain and not based on inclusion within a certain species. IMPORTANCE Representative type strains are commonly used to characterize bacterial species, yet species are phenotypically and genotypically heterogeneous. Conclusions about strain physiology and activity based on a single strain therefore may be inappropriate and misleading. When selecting strains for probiotic use, the assumption that all strains within a species share the same desired probiotic characteristics may result in selection of a strain that lacks the desired traits, and therefore makes a minimally effective or ineffective probiotic. Health-associated oral streptococci are promising candidates for anticaries probiotics, but strains need to be carefully selected based on observed phenotypes. We characterized the genotypes and anticaries phenotypes of strains from 10 species of oral streptococci and demonstrate poor correlation between genotype and phenotype across all species.Irina M. VelskoBrinta ChakrabortyMarcelle M. NascimentoRobert A. BurneVincent P. RichardsAmerican Society for MicrobiologyarticleStreptococcusgenomicsoral microbiologyphylogenetic analysisvariable phenotypesMicrobiologyQR1-502ENmSystems, Vol 3, Iss 6 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Streptococcus genomics oral microbiology phylogenetic analysis variable phenotypes Microbiology QR1-502
spellingShingle	Streptococcus genomics oral microbiology phylogenetic analysis variable phenotypes Microbiology QR1-502 Irina M. Velsko Brinta Chakraborty Marcelle M. Nascimento Robert A. Burne Vincent P. Richards Species Designations Belie Phenotypic and Genotypic Heterogeneity in Oral Streptococci
description	ABSTRACT Health-associated oral Streptococcus species are promising probiotic candidates to protect against dental caries. Ammonia production through the arginine deiminase system (ADS), which can increase the pH of oral biofilms, and direct antagonism of caries-associated bacterial species are desirable properties for oral probiotic strains. ADS and antagonistic activities can vary dramatically among individuals, but the genetic basis for these differences is unknown. We sequenced whole genomes of a diverse set of clinical oral Streptococcus isolates and examined the genetic basis of variability in ADS and antagonistic activities. A total of 113 isolates were included and represented 10 species: Streptococcus australis, A12-like, S. cristatus, S. gordonii, S. intermedius, S. mitis, S. oralis including S. oralis subsp. dentisani, S. parasanguinis, S. salivarius, and S. sanguinis. Mean ADS activity and antagonism on Streptococcus mutans UA159 were measured for each isolate, and each isolate was whole genome shotgun sequenced on an Illumina MiSeq. Phylogenies were built of genes known to be involved in ADS activity and antagonism. Several approaches to correlate the pan-genome with phenotypes were performed. Phylogenies of genes previously identified in ADS activity and antagonism grouped isolates by species, but not by phenotype. A genome-wide association study (GWAS) identified additional genes potentially involved in ADS activity or antagonism across all the isolates we sequenced as well as within several species. Phenotypic heterogeneity in oral streptococci is not necessarily reflected by genotype and is not species specific. Probiotic strains must be carefully selected based on characterization of each strain and not based on inclusion within a certain species. IMPORTANCE Representative type strains are commonly used to characterize bacterial species, yet species are phenotypically and genotypically heterogeneous. Conclusions about strain physiology and activity based on a single strain therefore may be inappropriate and misleading. When selecting strains for probiotic use, the assumption that all strains within a species share the same desired probiotic characteristics may result in selection of a strain that lacks the desired traits, and therefore makes a minimally effective or ineffective probiotic. Health-associated oral streptococci are promising candidates for anticaries probiotics, but strains need to be carefully selected based on observed phenotypes. We characterized the genotypes and anticaries phenotypes of strains from 10 species of oral streptococci and demonstrate poor correlation between genotype and phenotype across all species.
format	article
author	Irina M. Velsko Brinta Chakraborty Marcelle M. Nascimento Robert A. Burne Vincent P. Richards
author_facet	Irina M. Velsko Brinta Chakraborty Marcelle M. Nascimento Robert A. Burne Vincent P. Richards
author_sort	Irina M. Velsko
title	Species Designations Belie Phenotypic and Genotypic Heterogeneity in Oral Streptococci
title_short	Species Designations Belie Phenotypic and Genotypic Heterogeneity in Oral Streptococci
title_full	Species Designations Belie Phenotypic and Genotypic Heterogeneity in Oral Streptococci
title_fullStr	Species Designations Belie Phenotypic and Genotypic Heterogeneity in Oral Streptococci
title_full_unstemmed	Species Designations Belie Phenotypic and Genotypic Heterogeneity in Oral Streptococci
title_sort	species designations belie phenotypic and genotypic heterogeneity in oral streptococci
publisher	American Society for Microbiology
publishDate	2018
url	https://doaj.org/article/35f1bfbe8ca34df49f391dccf3ff60ec
work_keys_str_mv	AT irinamvelsko speciesdesignationsbeliephenotypicandgenotypicheterogeneityinoralstreptococci AT brintachakraborty speciesdesignationsbeliephenotypicandgenotypicheterogeneityinoralstreptococci AT marcellemnascimento speciesdesignationsbeliephenotypicandgenotypicheterogeneityinoralstreptococci AT robertaburne speciesdesignationsbeliephenotypicandgenotypicheterogeneityinoralstreptococci AT vincentprichards speciesdesignationsbeliephenotypicandgenotypicheterogeneityinoralstreptococci
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Species Designations Belie Phenotypic and Genotypic Heterogeneity in Oral Streptococci

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