Berry Michelle A, White Jeffrey D, Davis Timothy W, Jain Sunit, Johengen Thomas H, Dick Gregory J, Sarnelle Orlando, Denef Vincent J
Department of Ecology and Evolutionary Biology, University of Michigan Ann Arbor, MI, USA.
Department of Biology, Framingham State University Framingham, MA, USA.
Front Microbiol. 2017 Mar 8;8:365. doi: 10.3389/fmicb.2017.00365. eCollection 2017.
Oligotyping is a computational method used to increase the resolution of marker gene microbiome studies. Although oligotyping can distinguish highly similar sequence variants, the resulting units are not necessarily phylogenetically and ecologically informative due to limitations of the selected marker gene. In this perspective, we examine how oligotyping data is interpreted in recent literature, and we illustrate some of the method's constraints with a case study of the harmful bloom-forming cyanobacterium . We identified three oligotypes from a western Lake Erie bacterial community 16S rRNA gene (V4 region) survey that had previously clustered into one OTU. We found the same three oligotypes and two additional sequence variants in 46 cultures isolated from Michigan inland lakes spanning a trophic gradient. In Lake Erie, shifts in oligotypes corresponded to spatial nutrient gradients and temporal transitions in bloom toxicity. In the cultures, oligotypes showed preferential distributions for different trophic states, but genomic data revealed that the oligotypes identified in Lake Erie did not correspond to toxin gene presence. Thus, oligotypes could not be used for inferring toxic ecotypes. Most strikingly, oligotypes were not monophyletic. Our study supports the utility of oligotyping for distinguishing sequence types along certain ecological features, while it stresses that 16S rRNA gene sequence types may not reflect ecologically or phylogenetically cohesive populations. Therefore, we recommend that studies employing oligotyping or related tools consider these caveats during data interpretation.
寡核苷酸分型是一种用于提高标记基因微生物组研究分辨率的计算方法。尽管寡核苷酸分型能够区分高度相似的序列变体，但由于所选标记基因的局限性，所得出的分类单元在系统发育和生态学方面不一定具有信息价值。从这个角度出发，我们研究了近期文献中对寡核苷酸分型数据的解读方式，并通过对有害水华形成蓝藻的案例研究来说明该方法的一些局限性。我们从伊利湖西部细菌群落16S rRNA基因（V4区）调查中鉴定出三种寡核苷酸类型，这些类型之前被聚类到同一个操作分类单元中。我们在从密歇根州内陆湖泊分离出的46个跨越营养梯度的培养物中发现了相同的三种寡核苷酸类型以及另外两种序列变体。在伊利湖，寡核苷酸类型的变化与空间营养梯度以及水华毒性的时间转变相对应。在培养物中，寡核苷酸类型在不同营养状态下呈现出偏好性分布，但基因组数据显示，在伊利湖鉴定出的寡核苷酸类型与毒素基因的存在并无对应关系。因此，寡核苷酸类型不能用于推断有毒生态型。最显著的是，寡核苷酸类型并非单系的。我们的研究支持寡核苷酸分型在沿着某些生态特征区分序列类型方面的实用性，同时强调16S rRNA基因序列类型可能无法反映生态或系统发育上具有凝聚力的种群。因此，我们建议采用寡核苷酸分型或相关工具的研究在数据解读过程中考虑这些注意事项。
