Population structure of plasmid-containing strains of Streptococcus mutans, a member of the human indigenous biota

Abstract

There are suggestions that the phylogeny of Streptococcus mutans, a member of the human indigenous biota that is transmitted mostly mother to child, might parallel the evolutionary history of its human host. The relatedness and phylogeny of plasmid-containing strains of S. mutans were examined based on chromosomal DNA fingerprints (CDF), a hypervariable region (HVR) of a 5.6-kb plasmid, the rRNA gene intergenic spacer region (IGSR), serotypes, and the genotypes of mutacin I and II. Plasmid-containing strains were studied because their genetic diversity was twice as great as that of plasmid-free strains. The CDF of S. mutans from unrelated human hosts were unique, except those from Caucasians, which were essentially identical. The evolutionary history of the IGSR, with or without the serotype and mutacin characters, clearly delineated an Asian clade. Also, a continuous association with mutacin II could be reconstructed through an evolutionary lineage with the IGSR, but not for serotype e. DNA sequences from the HVR of the plasmid produced a well-resolved phylogeny that differed from the chromosomal phylogeny, indicating that the horizontal transfer of the plasmid may have occurred multiple times. The plasmid phylogeny was more congruent with serotype e than with mutacin II evolution, suggesting a possible functional correlation. Thus, the history of this three-tiered relationship between human, bacterium, and plasmid supported both coevolution and independent evolution.

FIG. 1.

Chromosomal-DNA fingerprints of plasmid-containing strains of S. mutans from unrelated individuals, restricted with HaeIII. (A) Strains from different ethnically/racially/geographically distinct hosts. (B) S. mutans from a Caucasian population from the United States and Australia. Strain CA143 contains a 0.9-kb insertion sequence. (C) Strain CH830, obtained from an individual from the southern region of China (Hainan province), displays a chromosomal-DNA fingerprint similar to that of strain CA96, a strain isolated from a Caucasian individual from Birmingham, AL. Lane λ, bacteriophage lambda cut with HindIII size standard.

FIG. 2.

Unrooted maximum-likelihood phylogeny of the cryptic 5.6-kb plasmid as inferred from HVR sequences (see Material and Methods for details of analysis). Taxa with names in blue represent strains with mutacin II, and those in black represent strains with mutacin I; taxa and branches in red represent strains and ancestral lineages with serotype e. One of two possible reconstructions is depicted for serotype e; the alternative possibility is that serotype e was independently derived for CH5A. The pairs of numbers on branches are bootstrap values: the first number is from a likelihood bootstrap analysis, and the second is from a weighted-parsimony bootstrap (1,000 replicates each). Hyphens and branches without numbers indicate bootstrap values that were below 50%. The branch lengths are proportional to the numbers of substitutions/site, as reconstructed using the HKY85+G likelihood model. Abbreviations for ethnicity of the human host: AF, African; AA, African American; CA, Caucasian American; CH, Chinese; JP, Japanese; BR, Brazilian; AM, Amazon Indian; SW, Swedish Caucasian; HI, Hispanic.

FIG. 3.

Maximum-likelihood phylogeny of IGSR sequences from strains with plasmids, rooted with IGSR Streptococcus ratti CCUG 27642 (see Materials and Methods for details of the analysis). Taxa and branches in blue represent strains with mutacin II; taxon names in red represent strains with serotype e. The triplets of numbers on branches are bootstrap values: the first two numbers are from weighted-parsimony analysis including or excluding, respectively, serotype and mutacin characters (2,000 and 1,000 bootstrap replications); the third is from a likelihood bootstrap (952 replications). When the serotype and mutacin characters were included and each was weighted the same as the set of DNA characters (i.e., the three data partitions were weighted equally), HI24 grouped with the AF199 cluster with a parsimony bootstrap value of 58%. Hyphens and branches without numbers indicate bootstrap values that were below 50%. The branch lengths are proportional to the numbers of substitutions/site as reconstructed using the HKY85+G likelihood model.