Institute of Mathematical Problems of Biology RAS-the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, 142290 Pushchino, Russia.
Structural and Functional Genomics Group, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", 142290 Pushchino, Russia.
Int J Mol Sci. 2020 Jan 31;21(3):944. doi: 10.3390/ijms21030944.
The need for a comparative analysis of natural metagenomes stimulated the development of new methods for their taxonomic profiling. Alignment-free approaches based on the search for marker -mers turned out to be capable of identifying not only species, but also strains of microorganisms with known genomes. Here, we evaluated the ability of genus-specific -mers to distinguish eight phylogroups of (A, B1, C, E, D, F, G, B2) and assessed the presence of their unique 22-mers in clinical samples from microbiomes of four healthy people and four patients with Crohn's disease. We found that a phylogenetic tree inferred from the pairwise distance matrix for unique 18-mers and 22-mers of 124 genomes was fully consistent with the topology of the tree, obtained with concatenated aligned sequences of orthologous genes. Therefore, we propose strain-specific "barcodes" for rapid phylotyping. Using unique 22-mers for taxonomic analysis, we detected microbes of all groups in human microbiomes; however, their presence in the five samples was significantly different. Pointing to the intraspecies heterogeneity of in the natural microflora, this also indicates the feasibility of further studies of the role of this heterogeneity in maintaining population homeostasis.
对自然宏基因组进行比较分析的需求刺激了用于对其进行分类分析的新方法的发展。基于寻找标记 - mers 的无比对方法不仅能够识别物种，还能够识别具有已知基因组的微生物菌株。在这里，我们评估了属特异性 -mers 区分 8 个（A、B1、C、E、D、F、G、B2） phylogroups 的能力，并评估了它们在来自四个健康人和四个克罗恩病患者微生物组的临床样本中的独特 22-mers 的存在。我们发现，从 124 个基因组的独特 18-mers 和 22-mers 的成对距离矩阵推断出的系统发育树与使用同源基因的串联比对序列获得的树的拓扑结构完全一致。因此，我们为快速分类提出了菌株特异性的“条形码”。使用独特的 22-mers 进行分类分析，我们在人类微生物组中检测到了所有组的微生物；然而，它们在五个样本中的存在存在显著差异。这表明了在自然微生物群中存在种内异质性，这也表明了进一步研究这种异质性在维持种群内稳态中的作用的可行性。
