Department of Ecology and Genetics, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.
Mol Biol Evol. 2020 Oct 1;37(10):3003-3022. doi: 10.1093/molbev/msaa135.
Dental calculus, the calcified form of the mammalian oral microbial plaque biofilm, is a rich source of oral microbiome, host, and dietary biomolecules and is well preserved in museum and archaeological specimens. Despite its wide presence in mammals, to date, dental calculus has primarily been used to study primate microbiome evolution. We establish dental calculus as a valuable tool for the study of nonhuman host microbiome evolution, by using shotgun metagenomics to characterize the taxonomic and functional composition of the oral microbiome in species as diverse as gorillas, bears, and reindeer. We detect oral pathogens in individuals with evidence of oral disease, assemble near-complete bacterial genomes from historical specimens, characterize antibiotic resistance genes, reconstruct components of the host diet, and recover host genetic profiles. Our work demonstrates that metagenomic analyses of dental calculus can be performed on a diverse range of mammalian species, which will allow the study of oral microbiome and pathogen evolution from a comparative perspective. As dental calculus is readily preserved through time, it can also facilitate the quantification of the impact of anthropogenic changes on wildlife and the environment.
牙垢，哺乳动物口腔微生物斑块生物膜的钙化形式，是口腔微生物组、宿主和饮食生物分子的丰富来源，并且在博物馆和考古标本中保存完好。尽管牙垢在哺乳动物中广泛存在，但迄今为止，牙垢主要用于研究灵长类动物微生物组的进化。我们通过使用 shotgun 宏基因组学来描述从大猩猩、熊和驯鹿等各种物种的口腔微生物组的分类和功能组成，将牙垢确立为研究非人类宿主微生物组进化的有价值的工具。我们在有口腔疾病证据的个体中检测到口腔病原体，从历史标本中组装近乎完整的细菌基因组，描述抗生素抗性基因，重建宿主饮食成分，并恢复宿主遗传特征。我们的工作表明，可以对多种哺乳动物物种进行牙垢的宏基因组分析，这将允许从比较的角度研究口腔微生物组和病原体的进化。由于牙垢可以随着时间的推移而轻易保存，因此它还可以促进量化人为变化对野生动物和环境的影响。
