Long-term evolution of Streptococcus mitis and Streptococcus pneumoniae leads to higher genetic diversity within rather than between human populations.

Autor: Davison, Charlotte, Tallman, Sam, de Ste-Croix, Megan, Antonio, Martin, Oggioni, Marco R., Kwambana-Adams, Brenda, Freund, Fabian, Beleza, Sandra
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Zdroj: PLoS Genetics; 6/6/2024, Vol. 20 Issue 6, p1-26, 26p
Abstrakt: Evaluation of the apportionment of genetic diversity of human bacterial commensals within and between human populations is an important step in the characterization of their evolutionary potential. Recent studies showed a correlation between the genomic diversity of human commensal strains and that of their host, but the strength of this correlation and of the geographic structure among human populations is a matter of debate. Here, we studied the genomic diversity and evolution of the phylogenetically related oro-nasopharyngeal healthy-carriage Streptococcus mitis and Streptococcus pneumoniae, whose lifestyles range from stricter commensalism to high pathogenic potential. A total of 119 S. mitis genomes showed higher within- and among-host variation than 810 S. pneumoniae genomes in European, East Asian and African populations. Summary statistics of the site-frequency spectrum for synonymous and non-synonymous variation and ABC modelling showed this difference to be due to higher ancestral bacterial population effective size (Ne) in S. mitis, whose genomic variation has been maintained close to mutation-drift equilibrium across (at least many) generations, whereas S. pneumoniae has been expanding from a smaller ancestral bacterial population. Strikingly, both species show limited differentiation among human populations. As genetic differentiation is inversely proportional to the product of effective population size and migration rate (Nem), we argue that large Ne have led to similar differentiation patterns, even if m is very low for S. mitis. We conclude that more diversity within than among human populations and limited population differentiation must be common features of the human microbiome due to large Ne. Author summary: The genetic variation of human-associated bacteria and the evolutionary mechanisms leading to that variation are crucial for the establishment of highly contextual interactions with their host, giving rise to phenotypes such as virulence. Here, we studied Streptococcus mitis and Streptococcus pneumoniae, who share a common ancestor but evolved lifestyles on different ends of the pathogenic potential spectrum: S. mitis is mainly commensal, whereas S. pneumoniae has high pathogenic potential. Genomic variation of worldwide healthy-carriage strains is considerably higher for S. mitis. We show this to be due to a larger ancestral population in S. mitis, whose population effective size (Ne) and mutation gain and loss (by genetic drift) have been kept stable over the generations. In contrast, S. pneumoniae population has expanded from an ancestral population with smaller Ne. We also observe low genetic differentiation among populations in both species. We deduce that this is due to large Ne which, even with limited dispersal rate as in S. mitis, leads to significant effective dispersal among populations. As both species' properties of Ne and dispersal are common among human-associated bacteria, more diversity within rather than among human populations and limited population differentiation must be common features of the human microbiome. [ABSTRACT FROM AUTHOR]
Databáze: Complementary Index
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