Measuring and understanding information storage and transfer in a simulated human gut microbiome

• Published in: PLoS computational biology Vol. 20; no. 9; p. e1012359
• Main Authors: Zoller, Hannah, Garcia Perez, Carlos, Betel Geijo Fernández, Javier, zu Castell, Wolfgang
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 17.09.2024
• Subjects: Agent based models; Biology and Life Sciences; Computational Biology; Computer and Information Sciences; Computer Simulation; Electronic data processing; Gastrointestinal Microbiome - physiology; Humans; Information storage and retrieval; Information Storage and Retrieval - methods; Medicine and Health Sciences; Methods; Microbiological research; Microbiota (Symbiotic organisms); Models, Biological; Physical Sciences; Research and Analysis Methods; Software; Germany
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.1012359

Considering biological systems as information processing entities and analyzing their organizational structure via information-theoretic measures has become an established approach in life sciences. We transfer this framework to a field of broad general interest, the human gut microbiome. We use BacArena, a software combining agent-based modelling and flux-balance analysis, to simulate a simplified human intestinal microbiome (SIHUMI). In a first step, we derive information theoretic measures from the simulated abundance data, and, in a second step, relate them to the metabolic processes underlying the abundance data. Our study provides further evidence on the role of active information storage as an indicator of unexpected structural change in the observed system. Besides, we show that information transfer reflects coherent behavior in the microbial community, both as a reaction to environmental changes and as a result of direct effective interaction. In this sense, purely abundance-based information theoretic measures can provide meaningful insight on metabolic interactions within bacterial communities. Furthermore, we shed light on the important however little noticed technical aspect of distinguishing immediate and delayed effects in the interpretation of local information theoretical measures.