Key Laboratory of Jiangxi Province for Numerical Simulation and Emulation Techniques, Gannan Normal University, Ganzhoiu, China.
Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education and Hunan Key Laboratory for Computation and Simulation in Science and Engineering, Xiangtan University, Xiangtan, China.
Front Cell Infect Microbiol. 2023 Jan 26;13:1117421. doi: 10.3389/fcimb.2023.1117421. eCollection 2023.
The species diversity of microbiomes is a cutting-edge concept in metagenomic research. In this study, we propose a multifractal analysis for metagenomic research.
Firstly, we visualized the chaotic game representation (CGR) of simulated metagenomes and real metagenomes. We find that metagenomes are visualized with self-similarity. Then we defined and calculated the multifractal dimension for the visualized plot of simulated and real metagenomes, respectively. By analyzing the Pearson correlation coefficients between the multifractal dimension and the traditional species diversity index, we obtain that the correlation coefficients between the multifractal dimension and the species richness index and Shannon diversity index reached the maximum value when q = 0, 1, and the correlation coefficient between the multifractal dimension and the Simpson diversity index reached the maximum value when q = 5. Finally, we apply our method to real metagenomes of the gut microbiota of 100 infants who are newborn and 4 and 12 months old. The results show that the multifractal dimensions of an infant's gut microbiomes can distinguish age differences.
There is self-similarity among the CGRs of WGS of metagenomes, and the multifractal spectrum is an important characteristic for metagenomes. The traditional diversity indicators can be unified under the framework of multifractal analysis. These results coincided with similar results in macrobial ecology. The multifractal spectrum of infants' gut microbiomes are related to the development of the infants.
微生物组的物种多样性是宏基因组研究的前沿概念。在这项研究中，我们提出了一种用于宏基因组研究的多重分形分析方法。
首先，我们可视化了模拟宏基因组和真实宏基因组的混沌游戏表示（CGR）。我们发现宏基因组具有自相似性。然后，我们分别定义并计算了模拟和真实宏基因组可视化图的多重分形维数。通过分析多重分形维数与传统物种多样性指数之间的皮尔逊相关系数，我们发现当 q = 0、1 时，多重分形维数与物种丰富度指数和香农多样性指数之间的相关系数达到最大值，当 q = 5 时，多重分形维数与辛普森多样性指数之间的相关系数达到最大值。最后，我们将我们的方法应用于 100 名新生儿和 4 个月和 12 个月大的婴儿肠道微生物组的真实宏基因组。结果表明，婴儿肠道微生物组的多重分形维数可以区分年龄差异。
宏基因组 WGS 的 CGR 之间存在自相似性，多重分形谱是宏基因组的一个重要特征。传统的多样性指标可以在多重分形分析框架下统一。这些结果与宏观生态学中的类似结果一致。婴儿肠道微生物组的多重分形谱与婴儿的发育有关。
