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.

本研究为一项双盲、随机、安慰剂对照试验，将由两歧双歧杆菌（B. bifidum）W23、乳双歧杆菌（B. lactis）W52以及乳酸乳球菌（Lc. Lactis）W58组成的益生菌混合物（商品名为Ecologic® Panda）给予妊娠最后6周的孕妇，并在其后代出生后的第一年持续给药。随访期间，研究人员在6年时间内从99名儿童身上采集粪便样本，采样时间点分别为：出生后第1周、第2周、第1个月、3个月、1岁、18个月、2岁及6岁。

细菌群落谱分析采用IS-pro技术完成：IS-pro通过16S-23S rRNA基因间区的长度实现细菌物种区分，并结合PCR引物的门特异性荧光标记完成即时分类。16S-23S rRNA基因间区的长度与序列均存在变异，使其非常适合复杂微生物群落的分析。

研究证实，IS-pro得到的菌群谱具有可重复性，且对峰强度值进行log2转换后，既可以识别相关菌群谱之间的细微差异，也可实现大规模菌群谱集的相关性分析。IS-pro不会产生传统意义上的测序序列数据，这意味着其无法达到下一代测序（next-generation sequencing, NGS）技术的分析细节，但序列数据已证实IS-pro在15个常见峰中的检测特异性，充分验证了该技术的有效性。

每份样本以一套微生物谱进行表征，该谱由带有颜色标记的峰组成。每个峰均对应一段特定的IS片段（以核苷酸数量为单位），并带有与特定微生物门类相对应的荧光颜色；峰的强度则反映PCR产物的相对含量（以相对荧光单位（relative fluorescence units, RFU）为单位）。每个峰被定义为一个操作分类单元（operational taxonomic unit, OTU），其对应峰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影响，并在下游分析中纳入丰度较低的菌群成员，研究人员对峰强度值进行了log2转换处理。

本研究公开共享IS-pro分析得到的原始数据集。