Boolean analysis reveals systematic interactions among low-abundance species in the human gut microbiome.

Authors:
Jens Christian Claussen, Jurgita Skiecevičienė, Jun Wang, Philipp Rausch, Tom H Karlsen, Wolfgang Lieb, John F Baines, Andre Franke, Marc-Thorsten Hütt
Year of publication:
2017
Volume:
13
Issue:
6
Issn:
1553-734X
Journal title abbreviated:
PLOS COMPUT BIOL
Journal title long:
PLoS computational biology / Public Library of Science [and] International Society for Computational Biology
Impact factor:
4.829
Abstract:
The analysis of microbiome compositions in the human gut has gained increasing interest due to the broader availability of data and functional databases and substantial progress in data analysis methods, but also due to the high relevance of the microbiome in human health and disease. While most analyses infer interactions among highly abundant species, the large number of low-abundance species has received less attention. Here we present a novel analysis method based on Boolean operations applied to microbial co-occurrence patterns. We calibrate our approach with simulated data based on a dynamical Boolean network model from which we interpret the statistics of attractor states as a theoretical proxy for microbiome composition. We show that for given fractions of synergistic and competitive interactions in the model our Boolean abundance analysis can reliably detect these interactions. Analyzing a novel data set of 822 microbiome compositions of the human gut, we find a large number of highly significant synergistic interactions among these low-abundance species, forming a connected network, and a few isolated competitive interactions.