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).
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Sequencing data are available at NCBI SRA under PRJNA541083.
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H.H.W. acknowledges funding from the NIH (grant nos. R01AI132403, R01DK118044), Burroughs Wellcome Fund (no. PATH 1016691), Bill & Melinda Gates Foundation (no. INV-000609), and the Schaefer Research Scholars Program for this work. R.U.S. is supported by a Fannie and John Hertz Foundation Fellowship and a NSF Graduate Research Fellowship (no. DGE-1644869). B.W.J. is supported in part by the NIH under Ruth L. Kirschstein National Research Service Award (NRSA) Institutional Research Training Grant (no. T32GM007367) and by the MD-PhD program at Columbia University. D.V. acknowledges funding from the NIH (grant nos. R01GM079759, R01DK118044).
The authors declare no competing interests.
Peer review information: Nicole Rusk was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.
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Ji, B.W., Sheth, R.U., Dixit, P.D. et al. Quantifying spatiotemporal variability and noise in absolute microbiota abundances using replicate sampling. Nat Methods 16, 731–736 (2019). https://doi.org/10.1038/s41592-019-0467-y
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