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.现代饮食不适应性与多种慢性疾病的发生密切相关。鉴于工业化社会中龋齿、慢性牙龈疾病等疾病的患病率更高，本研究旨在通过口腔微生物组（oral microbiome）解析不同生计策略对口腔健康及生理状态的影响。为控制环境、宿主遗传学等混淆变量，我们从菲律宾境内3对毗邻分布的狩猎采集者（hunter-gatherers）与传统农耕人群群体中采集了唾液样本。对唾液DNA进行深度鸟枪测序（deep shotgun sequencing）后，我们获得了高覆盖度的口腔微生物组及人类基因组数据。将该微生物组数据与公开的西式饮食人群数据进行比对后发现，核心物种的丰度比与生计策略显著相关：狩猎采集者与西式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。尽管狩猎采集者的口腔健康状况看似良好，但其体内优先检出的微生物中包含常被视为口腔致病菌的类群。对基因功能的判别分析显示，维生素B5（vitamin B5）自养型（autotrophy）与脲酶（urease）介导的pH调节分别是微生物组适配狩猎采集者饮食与西式饮食的潜在适应性机制。本研究结果表明，饮食结构的重大转变会筛选出不同的共生微生物（commensals）群落，并可能在现代口腔致病菌的演化出现中发挥了作用。