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Temporal microbiome road-maps guided by perturbations

View ORCID ProfileBeatriz García-Jiménez, Mark Wilkinson
doi: https://doi.org/10.1101/049510
Beatriz García-Jiménez
Biological Informatics Group, Center for Plant Biotechnology and Genomics (CBGP), UPM - INIA, 28223 Pozuelo de Alarcon (Madrid), Spain.
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Mark Wilkinson
Biological Informatics Group, Center for Plant Biotechnology and Genomics (CBGP), UPM - INIA, 28223 Pozuelo de Alarcon (Madrid), Spain.
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Abstract

Motivation There are few tools that allow longitudinal analysis of metagenomic data subjected to distinct perturbations.

Methods This study examines longitudinal metagenomics data modelled as a Markov Decision Process (MDP). Given an external perturbation, the MDP predicts the next microbiome state in a temporal sequence, selected from a finite set of possible microbiome states.

Results We examined three distinct datasets to demonstrate this approach. An MDP created for a vaginal microbiome time series generates a variety of behaviour policies. For example, that moving from a state associated with bacterial vaginosis to a healthier one, requires avoiding perturbations such as lubricant, sex toys, tampons and anal sex. The flexibility of our proposal is verified after applying MDPs to human gut and chick gut microbiomes, taking nutritional intakes, or salmonella and probiotic treatments, respectively, as perturbations. In the latter case, MDPs provided a quantitative explanation for why salmonella vaccine accelerates microbiome maturation in chicks. This novel analytical approach has applications in, for example, medicine where the MDP could suggest the sequence of perturbations (e.g. clinical interventions) to apply to follow the best path from any given starting state, to a desired (healthy) state, avoiding strongly negative states.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted April 20, 2016.
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Temporal microbiome road-maps guided by perturbations
Beatriz García-Jiménez, Mark Wilkinson
bioRxiv 049510; doi: https://doi.org/10.1101/049510
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Temporal microbiome road-maps guided by perturbations
Beatriz García-Jiménez, Mark Wilkinson
bioRxiv 049510; doi: https://doi.org/10.1101/049510

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