ArticleFrontiers in genetics2020
A Primer for Microbiome Time-Series Analysis.
Article in Frontiers in genetics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Viral Assemblages of a Hypersaline Estuary Show Divergent Responses to Freshwater and Temperature Disturbances.Environmental microbiology reports · 2026Article
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- Assessing the impact of interregional mobility on COVID19 spread in Spain using transfer entropy.Scientific reports · 2025Article
- Climate-driven succession in marine microbiome biodiversity and biogeochemical function.Nature communications · 2025Article
- Legacy of Repeated Cultivation Drives Cyclical Microbial Community Development in a Tropical Oxisol Soil.Microbial ecology · 2025Article
- Environmental community transcriptomics: strategies and struggles.Briefings in functional genomics · 2025Review
- Essential nucleic acid omics: a theoretical foundation for early-stage users.Frontiers in bioinformatics · 2025Review
- Time-series metagenomics reveals changing protistan ecology of a temperate dimictic lake.Microbiome · 2024Article
- Article
- Methodological Considerations in Longitudinal Analyses of Microbiome Data: A Comprehensive Review.Genes · 2023Review
- Exploring the Entropy Complex Networks with Latent Interaction.Entropy (Basel, Switzerland) · 2023Article
- Colonization-persistence trade-offs in natural bacterial communities.Proceedings. Biological sciences · 2023Article
- Symbiotic UCYN-A strains co-occurred with El Niño, relaxed upwelling, and varied eukaryotes over 10 years off Southern California.ISME communications · 2023Article
- Microbial Community Dynamics during a Harmful Chrysochromulina leadbeateri Bloom in Northern Norway.Applied and environmental microbiology · 2023Article
- Spatial and temporal metagenomics of river compartments reveals viral community dynamics in an urban impacted stream.Frontiers in microbiomes · 2023Article
- Capturing the dynamics of microbial interactions through individual-specific networks.Frontiers in microbiology · 2023Article
- Comparative evaluation of the fecal microbiota of adult hybrid pigs and Tibetan pigs, and dynamic changes in the fecal microbiota of hybrid pigs.Frontiers in immunology · 2023Article
- Exploring methods to summarize gut microbiota composition for microbiability estimation and phenotypic prediction in swine.Journal of animal science · 2022Article
- Review
- Statistical challenges in longitudinal microbiome data analysis.Briefings in bioinformatics · 2022Review
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Time-series can provide critical insights into the structure and function of microbial communities. The analysis of temporal data warrants statistical considerations, distinct from comparative microbiome studies, to address ecological questions. This primer identifies unique challenges and approaches for analyzing microbiome time-series. In doing so, we focus on (1) identifying compositionally similar samples, (2) inferring putative interactions among populations, and (3) detecting periodic signals. We connect theory, code and data via a series of hands-on modules with a motivating biological question centered on marine microbial ecology. The topics of the modules include characterizing shifts in community structure and activity, identifying expression levels with a diel periodic signal, and identifying putative interactions within a complex community. Modules are presented as self-contained, open-access, interactive tutorials in R and Matlab. Throughout, we highlight statistical considerations for dealing with autocorrelated and compositional data, with an eye to improving the robustness of inferences from microbiome time-series. In doing so, we hope that this primer helps to broaden the use of time-series analytic methods within the microbial ecology research community.
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