Population genetic structure and demographic history ofStreptococcus mutans(Bacteria: Streptococcaceae)

Abstract

Population genetic studies can contribute to current knowledge about the epidemiology of pathogens such as Streptococcus mutans, which is one of the most widely distributed bacteria in the world to be associated with human dental caries. In the present study, we investigated whether the population genetic structure of the species is clonal or recombinant, and we also evaluated the current levels of gene flow, admixed ancestry, and the hypothesis of an expansion of the bacteria within the last 10 000 years. Strains of S. mutans from C ordoba (Argentina) were obtained, with sequences of the genes aroE, gltA, gyrA, and lepC genes being aligned with those of strains from Japan, Thailand, and Finland. Most of our statistical analyses performed on the DNA matrix of 193 strains supported the existence of recombination at the intergene level. We also estimated the number of genetic clusters via Bayesian analyses, with three genetic clusters being detected in the four countries at different frequencies, as well as the number of strains with pure or admixed ancestry varying among countries. Argentina revealed 50% admixed strains, whereas these types of strains were present in only 8-19% of the other three countries analyzed. This result could be associated with the important human migration waves that Argentina has experienced, which may have mixed strains of S. mutans of different geographical origins. The demographic history was obtained using Extended Bayesian Skyline Plot anslysis, which showed important growth in the effective population size approximately 5000 years ago, coincident with the beginning of the dispersion of agriculture and a change to a diet rich in carbohydrates.

Genetic variation in the glucosyltransferase‐B gene of Streptococcus mutans and its relationship with caries experience in children from Córdoba, Argentina, and with strains from other countries

“…Compared with our previous study in which four housekeeping genes were used, the gtf-B gene is proportionally more variable (see table S1 and figure S1 by González-Ittig et al). 25 We also found here that 30.5% of the children presented values higher than ≥10 5 CFU/mL of S. mutans (see Appendix S1). When correlating these parameters, contrary to what was expected we did not detect associations between gtf-B genetic variability and levels of caries experience.…”

“…Twenty‐two genetic variants (alleles) were recovered from the 59 strains. Compared with our previous study in which four housekeeping genes were used, the gtf‐B gene is proportionally more variable (see table S1 and figure S1 by González‐Ittig et al) 25 . We also found here that 30.5% of the children presented values higher than ≥10 5 CFU/mL of S. mutans (see Appendix S1).…”

“…The shape of the network, with central alleles at high frequencies shared by several countries, resembles a typical network of species that have undergone recent demographic expansions 31 . In a previous study by our group, 25 using the housekeeping genes aro‐E, glt‐A, gyr‐A and lep‐C, we found that most of the composite sequence types were country‐specific, but there were also some shared between Argentina, Japan and Thailand, and to a lesser extent with Finland (see table S1 and figure S1 by González‐Ittig et al 25 ). Although in that work we used a Neighbour‐Net and not a traditional network as in the present study (Figure 2), the general pattern of both studies is comparable: many country‐specific alleles and a few shared by two or more countries.…”

“…Something similar was also suggested by Cornejo et al, 32 who used genome sequences corresponding to 57 strains from Brazil, Hong Kong, Iceland, Japan, South Africa, Turkey, the UK and the USA, and proposed that the S. mutans population started expanding exponentially approximately 10 000 years ago. González-Ittig et al 25 detected an important growth in the effective population size approximately 5000 years ago, coincident with the beginning of the dispersion of agriculture and a change to a diet rich in carbohydrates.…”

Genomic Distance-based Rapid Uncovering of Microbial Population Structures (GRUMPS): a reference free genomic data cleaning methodology

“…Theory. The genetic structure of a microbial population, or population structure, provides the organized distribution of genetic variations among a set of strains from different geographical locations and ecological niches inside the species 16,17 . Thus, the population structure of a set of strains can be leveraged to better understand the biological context of a bacterial species and the unique traits of subgroups within a given species 10,15 .…”