ArticleNature methods2019
Quantifying spatiotemporal variability and noise in absolute microbiota abundances using replicate sampling.
Article in Nature methods, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed.
- Probiotics-induced changes in gut microbial composition and its effects on cognitive performance after stress: exploratory analyses.Translational psychiatry · 2021Trial
- Insights into community profiles, environmental influence, and assembly mechanisms of oyster-associated bacteriome from Yueqing Bay, China via absolute quantitation by metabarcoding.Frontiers in microbiology · 2026Article
- Fecal exfoliome sequencing captures immune dynamics of the healthy and inflamed gut.Nature biotechnology · 2025Article
- Quantifying the relative contributions of bacterial and fungal communities to carcass decomposition using a quantitative microbiome profiling approach.NPJ biofilms and microbiomes · 2025Article
- Macroecological Laws Can Naturally Arise from Chaotic Internal Species Dynamics.bioRxiv : the preprint server for biology · 2025Article
- Microbiome diversity of low biomass skin sites is captured by metagenomics but not 16S amplicon sequencing.bioRxiv : the preprint server for biology · 2025Article
- Interactions between time on diet, antibiotic treatment, and liver abscess development on the fecal microbiome of beef cattle.Animal microbiome · 2025Article
- Quantifying compositional variability in microbial communities with FAVA.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Development of a quantitative metagenomic approach to establish quantitative limits and its application to viruses.Nucleic acids research · 2025Article
- SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome.Nature microbiology · 2025Article
- The quest for environmental analytical microbiology: absolute quantitative microbiome using cellular internal standards.Microbiome · 2025Review
- Article
- Bacteria Engineered to Produce Serotonin Modulate Host Intestinal Physiology.ACS synthetic biology · 2024Article
- Spatiotemporal dynamics during niche remodeling by super-colonizing microbiota in the mammalian gut.Cell systems · 2024Article
- SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome.bioRxiv : the preprint server for biology · 2024Article
- Dynamics of drinking water biofilm formation associated with Legionella spp. colonization.NPJ biofilms and microbiomes · 2024Article
- Long journey of 16S rRNA-amplicon sequencing toward cell-based functional bacterial microbiota characterization.iMetaOmics · 2024Review
- Antagonistic conflict between transposon-encoded introns and guide RNAs.Science (New York, N.Y.) · 2024Article
- Quantifying compositional variability in microbial communities with FAVA.bioRxiv : the preprint server for biology · 2024Article
- High-throughput microbial culturomics using automation and machine learning.Nature biotechnology · 2023Article
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7 authors.
Funding
Abstract
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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