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Characterising the role of microbial communities in human evolution and health is emerging as one of the most important and fascinating biomedical challenges of our times [1-4]. The oral microbiome, the complex ecosystem of microbes inhabiting the human mouth, is composed by hundreds of bacterial species, including landmark taxa like Neisseria, Prevotella, Streptococcus, Veillonella, Corynobacterium, Fusobacterium or Haemophilus [5]. The composition of the oral flora can however vary in terms of represented taxa and in terms of relative abundance between individuals given various factors including age, health status, ethnicity and diet. Notably, variations can be as subtle as relative abundance shifts in guilds of closely related species. These nuances are hard to characterize but may be crucial, as certain species or strain are commensal while their cognate species are pathogenic, like for Neisseria, Streptococcus, or Haemophilus. Indeed, the proliferation of pathogenic bacteria within the mouth may notably give rise to periodontitis, a common inflammatory disease affecting the tissues that support the teeth, known also to constitute a risk factor for cardiovascular disease [3].
While much is known about individual species associated with pathogenesis, the impacts of evolutionary changes in human diet and culture on commensal microbiota remain almost unknown [6]. In a recent study Adler and colleagues, showed that modern oral microbiotic ecosystems are markedly less diverse than historic populations, which might be contributing to chronic oral disease in post-industrial lifestyles [6]. In a study on the African Batwa pygmies, Nasidze et al. reported that hunter gatherers differ significantly from neighbouring agriculturalists in having fewer caries lesions and reduced tooth loss [7,8].
Differences in diet and lifestyle provide the most likely explanation for the greater prevalence of caries lesions and tooth loss but the role of the oral microbiota in this system remains poorly characterized as only a few metagenomic studies were conducted in this direction to date [5,6,8,9]. Moreover, the vast majority of these studies have focused mainly on bacterial composition using 16S rDNA diversity, thus ignoring the important link between the organism that are present and the functions they perform [4]. This connection can only be made by reconstructing partial or entire genomes from the community through metagenomic assembly. The assembly and analysis of multiple microbial metagenomes is a challenging and innovative field that only recently has become accessible to single research groups.
In this project in collaboration with the UCL Anthropology Dept., we applied deep whole-genome shotgun (WGS) sequencing for the analysis of the salivary microbiome diversity of three pairs of populations of hunter-gatherers and agricultural groups from similar environments in the Philippines. This set-up will allow us to test the impact of the genetic background and of the lifestyle - including diet - on the oral microbiota of these populations. Using the newest developments in deep sequencing technologies and metagenomic classification approaches, we investigate the phylogenetic diversity of these samples and characterized the genomic variation of taxa shared among them.