Hrovat Katarina, Dutilh Bas E, Medema Marnix H, Melkonian Chrats
Bioinformatics Group, Wageningen University and Research, 6708 PB Wageningen, The Netherlands.
Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands.
ISME Commun. 2024 Mar 8;4(1):ycae034. doi: 10.1093/ismeco/ycae034. eCollection 2024 Jan.
Plant-microbiome research plays a pivotal role in understanding the relationships between plants and their associated microbial communities, with implications for agriculture and ecosystem dynamics. Metabarcoding analysis on variable regions of the 16S ribosomal RNA (rRNA) gene remains the dominant technology to study microbiome diversity in this field. However, the choice of the targeted variable region might affect the outcome of the microbiome studies. In our analysis, we have evaluated whether the targeted variable region has an impact on taxonomic resolution in 16 plant-related microbial genera. Through a comparison of 16S rRNA gene variable regions with whole-genome data, our findings suggest that the V1-V3 region is generally a more suitable option than the widely used V3-V4 region for targeting microbiome analysis in plant-related genera. However, sole reliance on one region could introduce detection biases for specific genera. Thus, we are suggesting that while transitioning to full-length 16S rRNA gene and whole-genome sequencing for plant-microbiome analysis, the usage of genus-specific variable regions can achieve more precise taxonomic assignments. More broadly, our approach provides a blueprint to identify the most discriminating variable regions of the 16S rRNA gene for genera of interest.
植物微生物组研究在理解植物与其相关微生物群落之间的关系方面发挥着关键作用，对农业和生态系统动态具有重要意义。对16S核糖体RNA（rRNA）基因可变区进行元条形码分析仍然是该领域研究微生物组多样性的主导技术。然而，目标可变区的选择可能会影响微生物组研究的结果。在我们的分析中，我们评估了目标可变区是否对16个与植物相关的微生物属的分类分辨率有影响。通过将16S rRNA基因可变区与全基因组数据进行比较，我们的研究结果表明，对于植物相关属的微生物组分析，V1-V3区通常比广泛使用的V3-V4区更合适。然而，仅依赖一个区域可能会对特定属引入检测偏差。因此，我们建议在转向全长16S rRNA基因和全基因组测序进行植物微生物组分析时，使用属特异性可变区可以实现更精确的分类归属。更广泛地说，我们的方法提供了一个蓝图，用于识别感兴趣属的16S rRNA基因中最具区分性的可变区。
