Data from: Oral microbiomes from hunter-gatherers and traditional farmers reveal shifts in commensal balance and pathogen load linked to diet

Maladaptation to modern diets has been implicated in several chronic disorders. Given the higher prevalence of disease such as dental caries and chronic gum diseases in industrialized societies, we sought to investigate the impact of different subsistence strategies on oral health and physiology, as documented by the oral microbiome. To control for confounding variables such as environment and host genetics, we sampled saliva from three pairs of populations of hunter-gatherers and traditional farmers living in close proximity in the Philippines. Deep shotgun sequencing of salivary DNA generated high-coverage microbiomes along with human genomes. Comparing these microbiomes with publicly available data from individuals living on a Western diet revealed that abundance ratios of core species were significantly correlated with subsistence strategy, with hunter-gatherers and Westerners occupying either end of a gradient of Neisseria against Haemophilus, and traditional farmers falling in between. Species found preferentially in hunter-gatherers included microbes often considered as oral pathogens, despite their hosts' apparent good oral health. Discriminant analysis of gene functions revealed vitamin B5 autotrophy and urease-mediated pH regulation as candidate adaptations of the microbiome to the hunter-gatherer and Western diets, respectively. These results suggest that major transitions in diet selected for different communities of commensals and likely played a role in the emergence of modern oral pathogens.

机体对现代饮食的不适配现象，已被证实与多种慢性疾病存在关联。鉴于工业化社会中龋齿、慢性牙周病等疾病的患病率更高，本研究旨在探究不同生存策略对口腔健康与生理状态的影响，相关探究以口腔微生物组（oral microbiome）的特征作为佐证依据。为控制环境、宿主遗传学等混杂变量的影响，我们从菲律宾境内3组毗邻而居的狩猎采集者与传统农民群体中采集了唾液样本。对唾液DNA进行深度鸟枪法测序（deep shotgun sequencing）后，获得了高覆盖度的口腔微生物组与人类基因组数据。将本研究获得的微生物组数据与公开的西方饮食人群数据进行比对后发现，核心物种的丰度比值与生存策略显著相关：狩猎采集者与西方饮食人群分别处于奈瑟菌属（Neisseria）与嗜血杆菌属（Haemophilus）相对丰度梯度的两端，而传统农民群体则介于二者之间。尽管狩猎采集者宿主的口腔健康状况良好，但他们体内优先富集的微生物中包含了一些常被视为口腔致病菌的物种。对基因功能进行判别分析后发现，维生素B5自养与脲酶介导的pH调节分别可作为口腔微生物组适配狩猎采集者饮食与西方饮食的候选适应性特征。上述结果表明，饮食结构的重大转变会筛选出不同的共生菌群，且可能在现代口腔致病菌的演化出现过程中发挥了重要作用。