microPop: modelling microbial populations and communities in R

Helen Kettle, Grietje Holtrop, Petra Gisela Helen Louis, Harry J. Flint

Research output: Contribution to journalArticle

2 Citations (Scopus)
7 Downloads (Pure)

Abstract

1.Microbial communities perform highly dynamic and complex ecosystem functions that impact plants, animals and humans. Here we present an R-package, microPop, which is a dynamic model based on a functional representation of different microbiota.

2.microPop simulates the dynamics and interactions of microbial populations by solving a system of ordinary differential equations that are constructed automatically based on a description of the system.

3.Data frames for a number of microbial functional groups and default functions for rates of microbial growth, resource uptake, metabolite production are provided but can be modified or replaced by the user.

4.microPop can simulate growth in a single compartment (e.g. bio-reactor) or ‘compartments’ in series (e.g. human colon) or in a simple 1-d application (e.g. phytoplankton in a water column). Furthermore, a microbial functional group may contain multiple strains in order to study adaptation and diversity or parameter uncertainty. Also simple interactions between viruses (bacteriophages) and bacteria can be included in microPop.

5.microPop is hosted on CRAN and can be installed directly from within R. This paper describes version 1.3 of microPop. The code is also hosted on github for future development (https://github.com/HelenKettle/microPop).

This article is protected by copyright. All rights reserved.
Original languageEnglish
Pages (from-to)399-409
Number of pages11
JournalMethods in Ecology and Evolution
Volume9
Issue number2
Early online date14 Sep 2017
DOIs
Publication statusPublished - Feb 2018

Fingerprint

functional group
parameter uncertainty
bacteriophage
ecosystem function
dynamic models
bacteriophages
bioreactor
modeling
colon
microbial communities
microbial growth
microbial community
metabolite
virus
water column
phytoplankton
metabolites
uptake mechanisms
viruses
bacterium

Keywords

  • microbiota
  • colon
  • population dynamics
  • microbes
  • bacteria
  • rumen
  • gut
  • phtoplankton
  • methanogens
  • resource competition
  • microbial diversity
  • phages
  • virus
  • bacteriophage

Cite this

microPop: modelling microbial populations and communities in R. / Kettle, Helen; Holtrop, Grietje; Louis, Petra Gisela Helen; Flint, Harry J.

In: Methods in Ecology and Evolution, Vol. 9, No. 2, 02.2018, p. 399-409.

Research output: Contribution to journalArticle

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abstract = "1.Microbial communities perform highly dynamic and complex ecosystem functions that impact plants, animals and humans. Here we present an R-package, microPop, which is a dynamic model based on a functional representation of different microbiota.2.microPop simulates the dynamics and interactions of microbial populations by solving a system of ordinary differential equations that are constructed automatically based on a description of the system.3.Data frames for a number of microbial functional groups and default functions for rates of microbial growth, resource uptake, metabolite production are provided but can be modified or replaced by the user.4.microPop can simulate growth in a single compartment (e.g. bio-reactor) or ‘compartments’ in series (e.g. human colon) or in a simple 1-d application (e.g. phytoplankton in a water column). Furthermore, a microbial functional group may contain multiple strains in order to study adaptation and diversity or parameter uncertainty. Also simple interactions between viruses (bacteriophages) and bacteria can be included in microPop.5.microPop is hosted on CRAN and can be installed directly from within R. This paper describes version 1.3 of microPop. The code is also hosted on github for future development (https://github.com/HelenKettle/microPop).This article is protected by copyright. All rights reserved.",
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