Indugu Nagaraju, Bittinger Kyle, Kumar Sanjay, Vecchiarelli Bonnie, Pitta Dipti
Department of Clinical Studies, University of Pennsylvania , Kennett Square, PA , United States of America.
Department of Microbiology and Department of Biostatistics and Epidemiology, University of Pennsylvania , Philadelphia, PA , United States of America.
PeerJ. 2016 Feb 4;4:e1599. doi: 10.7717/peerj.1599. eCollection 2016.
Next generation sequencing (NGS) technology is a widely accepted tool used by microbial ecologists to explore complex microbial communities in different ecosystems. As new NGS platforms continue to become available, it becomes imperative to compare data obtained from different platforms and analyze their effect on microbial community structure. In the present study, we compared sequencing data from both the 454 and Ion Torrent (PGM) platforms on the same DNA samples obtained from the rumen of dairy cows during their transition period. Despite the substantial difference in the number of reads, error rate and length of reads among both platforms, we identified similar community composition between the two data sets. Procrustes analysis revealed similar correlations (M (2) = 0.319; P = 0.001) in the microbial community composition between the two platforms. Both platforms revealed the abundance of the same bacterial phyla which were Bacteroidetes and Firmicutes; however, PGM recovered an additional four phyla. Comparisons made at the genus level by each platforms revealed differences in only a few genera such as Prevotella, Ruminococcus, Succiniclasticum and Treponema (p < 0.05; chi square test). Collectively, we conclude that the output generated from PGM and 454 yielded concurrent results, provided stringent bioinformatics pipelines are employed.
下一代测序（NGS）技术是微生物生态学家广泛使用的一种工具，用于探索不同生态系统中的复杂微生物群落。随着新的NGS平台不断问世，比较从不同平台获得的数据并分析它们对微生物群落结构的影响变得势在必行。在本研究中，我们比较了从处于过渡期的奶牛瘤胃中获取的相同DNA样本在454平台和离子激流（PGM）平台上的测序数据。尽管两个平台在读取数、错误率和读取长度上存在显著差异，但我们在两个数据集之间鉴定出了相似的群落组成。普氏分析显示两个平台之间微生物群落组成具有相似的相关性（M(2)=0.319；P=0.001）。两个平台都显示出相同细菌门类的丰度，即拟杆菌门和厚壁菌门；然而，PGM还检测到另外四个门类。每个平台在属水平上的比较仅显示出少数几个属存在差异，如普雷沃氏菌属、瘤胃球菌属、琥珀酸裂解菌属和密螺旋体属（p<0.05；卡方检验）。总体而言，我们得出结论，只要采用严格的生物信息学流程，PGM和454产生的结果是一致的。
