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Deep learning predicts microbial interactions from self-organized spatiotemporal patterns.

Abstract：

:Microbial communities organize into spatial patterns that are largely governed by interspecies interactions. This phenomenon is an important metric for understanding community functional dynamics, yet the use of spatial patterns for predicting microbial interactions is currently lacking. Here we propose supervised deep learning as a new tool for network inference. An agent-based model was used to simulate the spatiotemporal evolution of two interacting organisms under diverse growth and interaction scenarios, the data of which was subsequently used to train deep neural networks. For small-size domains (100 µm × 100 µm) over which interaction coefficients are assumed to be invariant, we obtained fairly accurate predictions, as indicated by an average R2 value of 0.84. In application to relatively larger domains (450 µm × 450 µm) where interaction coefficients are varying in space, deep learning models correctly predicted spatial distributions of interaction coefficients without any additional training. Lastly, we evaluated our model against real biological data obtained using Pseudomonas fluorescens and Escherichia coli co-cultures treated with polymeric chitin or N-acetylglucosamine, the hydrolysis product of chitin. While P. fluorescens can utilize both substrates for growth, E. coli lacked the ability to degrade chitin. Consistent with our expectations, our model predicted context-dependent interactions across two substrates, i.e., degrader-cheater relationship on chitin polymers and competition on monomers. The combined use of the agent-based model and machine learning algorithm successfully demonstrates how to infer microbial interactions from spatially distributed data, presenting itself as a useful tool for the analysis of more complex microbial community interactions.

journal_name

Comput Struct Biotechnol J

journal_title

Computational and structural biotechnology journal

authors

Lee JY,Sadler NC,Egbert RG,Anderton CR,Hofmockel KS,Jansson JK,Song HS

doi

10.1016/j.csbj.2020.05.023

subject

Has Abstract

pub_date

2020-05-29 00:00:00

pages

1259-1269

issn

2001-0370

pii

S2001-0370(20)30286-5

journal_volume

pub_type

杂志文章

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Deep learning predicts microbial interactions from self-organized spatiotemporal patterns.