Data from: Metatranscriptomics of the human oral microbiome during health and disease

The human microbiome plays important roles in health, but when disrupted these same indigenous microbes can cause disease. The composition of the microbiome changes during the transition from health to disease; however, these changes are often not conserved among patients. Since microbiome-associated diseases like periodontitis cause similar patient symptoms despite inter-patient variability in microbial community composition, we hypothesized that human-associated microbial communities undergo conserved changes in metabolism during disease. Here we used patient-matched healthy and diseased samples to compare gene expression of 160,000 genes in healthy and diseased periodontal communities. We show that healthy and diseased communities exhibit defined differences in metabolism that are conserved between patients. In contrast, individual species metabolic gene expression was highly variable between patients. These results demonstrate that despite high inter-patient variability in microbial composition, diseased communities display conserved metabolic profiles that are generally accomplished by a patient-specific cohort of microbes.人类微生物组（human microbiome）在机体健康中发挥着关键作用，但当其稳态被打破时，这些固有微生物同样可引发疾病。微生物组的组成会在从健康向疾病转归的过程中发生改变；然而，这类改变往往在不同患者间并不保守。尽管牙周炎（periodontitis）这类与微生物组相关的疾病，在患者间的微生物群落组成存在个体差异，但患者的临床症状却较为相似，因此我们提出假设：与人类相关的微生物群落，在疾病状态下会发生保守性的代谢改变。本研究采用患者匹配的健康与患病样本，对比了健康与患病牙周群落中160,000个基因的表达情况。研究结果显示，健康与患病的微生物群落存在明确的代谢差异，且这类差异在不同患者间具有保守性。与之相反，单个物种的代谢基因表达在患者间呈现高度异质性。本研究结果表明，尽管微生物组成在患者间存在较高的个体差异，但患病的微生物群落仍呈现出保守的代谢特征，而这类特征通常由患者特异性的微生物类群所介导实现。