Stochastic logistic models reproduce experimental time series of microbial communities

Abstract
Data availability
Article and author information
Metrics

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 .

The following previously published data sets were used

(2014) Host lifestyle affects human microbiota on daily timescales
EBI/ENA database, PRJEB6518.

https://www.ebi.ac.uk/ena/data/view/PRJEB6518
(2018) High resolution time series reveals cohesive but short-lived communities in coastal plankton
Electronic supplementary material.

https://www.nature.com/articles/s41467-017-02571-4#additional-information
1. Caporaso JG
2. Lauber CL
3. Costello EK
4. Berg-Lyons D
5. Gonzalez A
6. Stombaugh J
7. Knights D
8. Gajer P
9. Ravel J
10. Fierer N
11. Gordon JI
12. Knight R
(2011) Moving Pictures of the Human Microbiome
MG-RAST, 4457768.3-4459735.3.

https://www.mg-rast.org/mgmain.html?mgpage=search&search=MG-RAST:4457768.3-4459735.3

Article and author information

Author details

Lana Descheemaeker

Physics department, Vrije Universiteit Brussel, Brussel, Belgium

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-8732-7051
Sophie de Buyl

Physics department, Vrije Universiteit Brussel, Brussel, Belgium

For correspondence
sdebuyl@vub.be

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-3314-9616

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.

Copyright

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.