BACKGROUND Evidence for a role of human gut microbiota in multiple sclerosis (MS) risk is mounting, yet large variability is seen across studies. This is, in part, due to the lack of standardization of study protocols, sample collection methods, and sequencing approaches. OBJECTIVE This study aims to address the effect of a household experimental design, sample collection, and sequencing approaches in a gut microbiome study in MS subjects from a multi-city study population. METHODS We analyzed 128 MS patient and cohabiting healthy control pairs from the International MS Microbiome Study (iMSMS). A total of 1005 snap-frozen or desiccated Q-tip stool samples were collected and evaluated using 16S and shallow whole-metagenome shotgun sequencing. RESULTS The intra-individual variance observed by different collection strategies was dramatically lower than inter-individual variance. Shallow shotgun highly correlated with 16S sequencing. Participant house and recruitment site accounted for the two largest sources of microbial variance, while higher microbial similarity was seen in household-matched participants as hypothesized. A significant proportion of the variance in dietary intake was also dominated by geographic distance. CONCLUSION A household pair study largely overcomes common inherent limitations and increases statistical power in population-based microbiome studies.

中文翻译：

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家庭配对设计可减少多发性硬化症多城市肠道微生物组研究的差异并提高能力

背景 关于人类肠道微生物群在多发性硬化症 (MS) 风险中的作用的证据越来越多，但研究中发现了很大的变异性。这部分是由于研究方案、样本收集方法和测序方法缺乏标准化。目的 本研究旨在探讨家庭实验设计、样本收集和测序方法在多城市研究人群的 MS 受试者肠道微生物组研究中的影响。方法 我们分析了来自国际 MS 微生物组研究 (iMSMS) 的 128 名 MS 患者和同居健康对照对。共收集了 1005 个速冻或干燥的 Q-tip 粪便样本，并使用 16S 和浅全宏基因组鸟枪法测序进行了评估。结果不同收集策略观察到的个体内差异显着低于个体内差异。浅霰弹枪与 16S 测序高度相关。参与者住所和招募地点是微生物变异的两个最大来源，而假设的家庭匹配参与者中的微生物相似性较高。饮食摄入量差异的很大一部分也受地理距离支配。结论 家庭配对研究在很大程度上克服了常见的固有局限性，并提高了基于人群的微生物组研究的统计功效。正如假设的那样，在家庭匹配的参与者中发现了更高的微生物相似性。饮食摄入量差异的很大一部分也受地理距离支配。结论 家庭配对研究在很大程度上克服了常见的固有局限性，并提高了基于人群的微生物组研究的统计功效。正如假设的那样，在家庭匹配的参与者中发现了更高的微生物相似性。饮食摄入量差异的很大一部分也受地理距离支配。结论 家庭配对研究在很大程度上克服了常见的固有局限性，并提高了基于人群的微生物组研究的统计功效。