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应性已被证实与多种慢性病症相关。鉴于工业化社会中龋齿与慢性牙周病的患病率显著更高，本研究旨在探究不同生计策略对口腔健康与生理状态的影响，相关影响可通过口腔微生物组（oral microbiome）得以反映。为控制环境、宿主遗传等混杂变量，我们从菲律宾境内三对毗邻居住的狩猎采集者与传统农耕人群群体中采集了唾液样本。通过对唾液DNA进行深度鸟枪测序，我们获得了高覆盖度的口腔微生物组与人类基因组数据。将上述微生物组数据与公开的西方饮食人群样本数据进行对比后发现，核心菌种的丰度比与生计策略显著相关：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，而传统农耕人群则介于二者之间。尽管狩猎采集者宿主的口腔健康状态看似良好，但他们体内优先富集的菌种中包含了常被视作口腔致病菌的微生物。对基因功能进行判别分析后结果显示，维生素B5自养特性与尿素酶介导的pH调控，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机制。上述结果表明，饮食的重大转型会筛选出不同的共生菌群群落，且可能在现代口腔致病菌的出现过程中发挥了作用。