Stochastic logistic models reproduce experimental time series of microbial communities
Abstract
We analyze properties of experimental microbial time series, from plankton and the human microbiome, and investigate whether stochastic generalized Lotka-Volterra models could reproduce those properties. We show that this is the case when the noise term is large and a linear function of the species abundance, while the strength of the self-interactions varies over multiple orders of magnitude. We stress the fact that all the observed stochastic properties can be obtained from a logistic model, i.e. without interactions, even the niche character of the experimental time series. Linear noise is associated with growth rate stochasticity, which is related to changes in the environment. This suggests that fluctuations in the sparsely sampled experimental time series may be caused by extrinsic sources.
Data availability
All data used in this study is available at https://github.com/lanadescheemaeker/logistic_models .
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Host lifestyle affects human microbiota on daily timescalesEBI/ENA database, PRJEB6518.
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Moving Pictures of the Human MicrobiomeMG-RAST, 4457768.3-4459735.3.
Article and author information
Author details
Funding
Vrije Universiteit Brussel (SRP31)
- Lana Descheemaeker
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Sandeep Krishna, National Centre for Biological Sciences‐Tata Institute of Fundamental Research, India
Version history
- Received: January 31, 2020
- Accepted: July 20, 2020
- Accepted Manuscript published: July 20, 2020 (version 1)
- Version of Record published: August 6, 2020 (version 2)
Copyright
© 2020, Descheemaeker & de Buyl
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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