Department of Systems Biology, Columbia University, New York, NY, USA.
Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, NY, USA.
Nat Methods. 2019 Aug;16(8):731-736. doi: 10.1038/s41592-019-0467-y. Epub 2019 Jul 15.
Metagenomic sequencing has enabled detailed investigation of diverse microbial communities, but understanding their spatiotemporal variability remains an important challenge. Here, we present decomposition of variance using replicate sampling (DIVERS), a method based on replicate sampling and spike-in sequencing. The method quantifies the contributions of temporal dynamics, spatial sampling variability, and technical noise to the variances and covariances of absolute bacterial abundances. We applied DIVERS to investigate a high-resolution time series of the human gut microbiome and a spatial survey of a soil bacterial community in Manhattan's Central Park. Our analysis showed that in the gut, technical noise dominated the abundance variability for nearly half of the detected taxa. DIVERS also revealed substantial spatial heterogeneity of gut microbiota, and high temporal covariances of taxa within the Bacteroidetes phylum. In the soil community, spatial variability primarily contributed to abundance fluctuations at short time scales (weeks), while temporal variability dominated at longer time scales (several months).
宏基因组测序技术使人们能够深入研究多样化的微生物群落，但要了解其时空变异性仍然是一个重要的挑战。在这里，我们提出了一种基于重复采样和添加测序的方法，即基于重复采样和添加测序的方差分解(DIVERS)。该方法定量评估了时间动态、空间采样变异性和技术噪声对绝对细菌丰度的方差和协方差的贡献。我们应用 DIVERS 来研究人类肠道微生物组的高分辨率时间序列和曼哈顿中央公园土壤细菌群落的空间调查。我们的分析表明，在肠道中，技术噪声几乎主导了近一半检测到的分类群的丰度变化。DIVERS 还揭示了肠道微生物组的大量空间异质性，以及拟杆菌门内分类群的高时间协方差。在土壤群落中，空间变异性主要导致了短时间尺度(几周)的丰度波动，而时间变异性在较长时间尺度(几个月)上占主导地位。
