Perspective

The ISME Journal (2015) 9, 533–541; doi:10.1038/ismej.2014.147; published online 22 August 2014

Biotic interactions and temporal dynamics of the human gastrointestinal microbiota

Pål Trosvik1, Eric Jacques de Muinck1 and Nils Christian Stenseth1

1Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway

Correspondence: P Trosvik, Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo 0316, Norway. E-mail: pal.trosvik@ibv.uio.no

Received 17 February 2014; Revised 3 July 2014; Accepted 9 July 2014
Advance online publication 22 August 2014

Top

Abstract

The human gastrointestinal (GI) microbiota is important to human health and imbalances or shifts in the gut microbial community have been linked to many diseases. Most studies of the GI microbiota only capture snapshots of this dynamic community at one or a few time points. Although this is valuable in terms of providing knowledge of community composition and variability between individuals, it does not provide the foundation for going beyond descriptive studies and toward truly predictive ecological models. In order to achieve this goal, we need longitudinal data of appropriate temporal and taxonomic resolution, so that established time series analysis tools for identifying and quantifying putative interactions among community members can be used. Here, we present new analyses of existing data to illustrate the potential usefulness of this approach. We discuss challenges related to sampling and data processing, as well as analytical approaches and considerations for future studies of the GI microbiota and other complex microbial systems.