Longitudinal profiling of non-disease individuals. Microbiota data.

In order to use the microbiota as potential biomarker the definition of a normal microbiota with measurable characteristics needs to be established. Here we longitudinally profiled the fecal microbiota of a normal Swedish population with no clinical evidence of disease using both shotgun metagenomics and 16S rRNA gene sequencing to determine compositional and functional variation over the course of one year. Our analyses confirmed that inter-individual differences are larger than intra-individual variation for the composition of gut microbiota, and we identified gene richness and abundance of Faecalibacteriusm prausnitzii, and Bifidobacterium species as stabilizing factors of the gut microbiota in this population. However, the abundance of different microbial species exhibited different levels of intra-individual variability, which was largest for facultative anaerobes and oxygen tolerant bacteria. These bacteria varied extensively in abundance also in individuals with high compositional stability. Therefore, we conclude that repeated sampling is required to account for the normal intra-individual variation of the gut microbiota and allow a more reliable quantification of microbial biomarkers and suggest that the concept of gut microbiota dysbiosis based on the expansion of rare taxa needs to be updated as these may bloom in normal individuals as well.

为将微生物群（microbiota）用作潜在生物标志物（biomarker），亟需建立具备可测量特征的正常微生物群定义。本研究对一群无临床疾病证据的瑞典正常人群开展了为期一年的纵向粪便微生物群分析，采用鸟枪宏基因组学（shotgun metagenomics）与16S核糖体RNA基因测序（16S rRNA gene sequencing）技术，解析肠道微生物群的组成与功能在一年周期内的变化特征。分析结果证实，肠道微生物群组成的个体间差异显著高于个体内变异；本研究还鉴定出基因丰富度、普拉梭菌（Faecalibacterium prausnitzii）及双歧杆菌（Bifidobacterium）物种的丰度可作为该人群肠道微生物群的稳定因子。然而，不同微生物物种的丰度所呈现的个体内变异水平存在差异，其中兼性厌氧菌与耐氧细菌的个体内变异程度最高。此类细菌的丰度在肠道组成稳定性较高的个体中同样存在显著波动。因此，本研究认为，需通过重复采样以覆盖肠道微生物群的正常个体内变异，从而实现微生物标志物的更可靠定量；同时建议更新基于稀有类群扩增的肠道微生物群失调概念，因为这类类群在正常个体中同样可能出现丰度激增。