SAMBA: Structure-Learning of Aquaculture Microbiomes Using a Bayesian-Network Approach

Abstract

AbstractSummaryLike in other animals, the gut microbiome of fishes contains thousands of microbial species that establish a complex network of relationships among each other and with the host. These interrelationships are shaped by biotic and abiotic factors, but little is known about how they evolved and how they are regulated by the environment, farmers and breeders. Herein, we introduce SAMBA (Structure-Learning ofAquacultureMicrobiomes Using aBayesian-NetworkApproach), the software implementation of a Bayesian network model for investigating how fish pan-microbiomes and all other variables of a given aquaculture system are related each to other. SAMBA is powered by a Bayesian network trainable model that learns the network structure of an aquaculture system using information from distinct biotic and abiotic variables of importance in fish farming, with special focus on microbial data provided from 16S amplicon sequencing. SAMBA accepts both qualitative and quantitative variables and convincingly deals with the differences in microbial composition derived by the technical or biological variation among microbiomes of distinct specimens. To this end, SAMBA is implemented with a variety of tools to pre-analyze the data and chose a distribution (log-normal, binomial, etc.) to build and train the Bayesian network model. Once the model has been created and validated, the user can interrogate the model and obtain information about the modelled system in two different modes: Report and Prediction. Using the Report mode SAMBA reports how the pan-microbiome and all other variables involved in the modelled aquaculture system influence each other and what are the conditional probabilities of each relation. Under the Prediction mode, the application predicts how the diversity and functional profile of the pan-microbiome would likely change depending on any change made on other variables. Finally, SAMBA implements a comprehensive graphical network editor allowing to navigate, edit and export outcomes. We tested and validated the performance of SAMBA using microbial community standards and gut microbiota communities of farmed gilthead sea bream (Sparus aurata) from different feeding trials.Availability and implementationSAMBA is a web-based solution for network analysis. The backend component is a workflow implemented in R and Python using third party software dependencies while the front end component is the environment of graphical user interfaces implemented to manage SAMBA. The source code of SAMBA, the datasets to test it and instructions to execute the application are available athttps://github.com/biotechvana/SAMBA.Contactbeatriz.soriano@biotechvana.com,jaime.perez.sanchez@csic.esSupplementary InformationSupplementary data are available atBioinformaticsonline.