Raw data microbiota development Panda Study (part 3)

In a double-blind, randomized, placebo-controlled trial, a probiotic mixture consisting of B. bifidum W23, B. lactis W52 and Lc. Lactis W58 (Ecologic® Panda) was administered to pregnant women during the last 6 weeks of pregnancy and to their offspring during the first year of life. During follow-up, faecal samples were collected from 99 children over a 6-year period with the following time points: first week, second week, first month, three months, first year, eighteen months, two years and six years. Bacterial profiling was performed by IS-pro. IS-pro combines bacterial species differentiation by the length of the 16S-23S rRNA interspace region with instant taxonomic classification by phylum-specific fluorescent labeling of PCR-primers. The 16S-23S rRNA IS region is variable in size and sequence, making it well suitable for analysis of complex communities. It was demonstrated that profiles are reproducible and that log2 transformation enables both the identification of slight variations between related profiles, as well as correlation analysis of large sets of profiles. Is-pro does not generate sequence data in a traditional sense. This means IS-pro cannot achieve the same level of detail as next-generation sequencing techniques, although sequence data confirmed specificity of IS-pro in 15 common peaks, underlining the validity of the technique. Each sample is represented by a microbial profile, consisting of color-labeled peaks. Each peak is characterized by a specific IS fragment (measured in number of nucleotides) and a color related to a specific phylum group. The intensity of peaks reflects the quantity of PCR product (measured in relative fluorescence units (RFU)). Each peak is designated as an operational taxonomic unit (OTU) and its corresponding intensity as abundance. Intensity values are log2 transformed in order to compact the range of variation in peak heights, to reduce the dominance of abundant peaks and to include less abundant species of the microbiota in downstream analyses. Here we share the raw data of the IS-pro analysis.

本数据集来自一项双盲、随机、安慰剂对照试验：研究人员将由两歧双歧杆菌（B. bifidum W23）、乳酸双歧杆菌（B. lactis W52）及乳酸乳球菌（Lc. Lactis W58）组成的益生菌混合物（商品名Ecologic® Panda）给予妊娠最后6周的孕妇，以及其后代在出生后第一年服用。在随访期间，研究人员在6年时间内从99名儿童身上收集了粪便样本，采样时间点分别为第1周、第2周、第1个月、3个月、1岁、18个月、2岁及6岁。细菌谱分析采用IS-pro技术：该技术结合了基于16S-23S核糖体RNA（rRNA）间隔区长度的细菌物种区分方法，以及通过PCR引物的门特异性荧光标记实现的即时分类学鉴定。16S-23S rRNA间隔区（IS区）的长度与序列均存在变异性，使其非常适用于复杂菌群群落的分析。研究证实，该微生物谱图具有可重复性，且log2转化既可以识别相关谱图间的细微差异，也可支持大规模谱图集的相关性分析。IS-pro不会生成传统意义上的序列数据，因此无法达到下一代测序（next-generation sequencing）技术的细节分辨率，但已有序列数据证实其在15个常见峰中的特异性，验证了该技术的有效性。每份样本以微生物谱图的形式呈现，由带颜色标记的峰组成。每个峰对应一段特定的IS片段（以核苷酸数量计），以及与特定菌群门相关的颜色。峰的强度反映PCR产物的相对含量（以相对荧光单位RFU, relative fluorescence units计）。每个峰被定义为一个操作分类单元（OTU, operational taxonomic unit），其对应强度即为该类群的丰度。为压缩峰高的变异范围、降低高丰度峰的主导性，并在下游分析中纳入丰度较低的菌群成员，研究人员对强度值进行了log2转化。本研究共享IS-pro分析的原始数据。