Hafez, A. | Search bioRxiv

bioRxiv2022

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

In aquaculture systems, microbiomes of farmed fishes may contain thousands of bacterial taxa that establish complex networks of interactions among each other and among the host and the environment. Gut microbiomes in many fish species consist of thousands of bacterial taxa that interact among each other, their environment, and the host. These complex networks of interactions are regulated by a diverse range of factors, yet little is known about the hierarchy of these interactions. Here, we introduce SAMBA (Structure-Learning of Aquaculture Microbiomes using a Bayesian Approach), a computational tool that uses a unified Bayesian network approach to model the network structure of fish gut microbiomes and their interactions with biotic and abiotic variables associated with typical aquaculture systems. SAMBA accepts input data on microbial abundance from 16S rRNA amplicons as well as continuous and categorical information from distinct farming conditions. From this, SAMBA can create and train a network model scenario that can be used to: i) infer information how specific farming conditions influence the diversity of the gut microbiome or pan-microbiome, and ii) predict how the diversity and functional profile of that microbiome would change under other experimental variables. SAMBA also allows the user to visualize, manage, edit, and export the acyclic graph of the modelled network. Our study presents examples and test results of bayesian network scenarios created by SAMBA using data from: a) a microbial synthetic experiment; and b) the pan-microbiome of the gilthead sea bream (Sparus aurata) under different experimental feeding trials. It is worth noting that the usage of SAMBA is not limited to aquaculture systems and can be used for modelling microbiome-host network relationships in any vertebrate organism, including humans, in any system and/or ecosystem.

bioinformatics↗

bioRxiv2019

Genome Sequencing and Transcriptome Analysis Reveal Recent Species-specific Gene Duplications in the Plastic Gilthead Sea Bream

Gilthead sea bream is an economically important fish species that is remarkably well-adapted to farming and changing environments. Understanding the genomic basis of this plasticity will serve to orientate domestication and selective breeding towards more robust and efficient fish. To address this goal, a draft genome assembly was reconstructed combining short- and long-read high-throughput sequencing with genetic linkage maps. The assembled unmasked genome spans 1.24 Gb of an expected 1.59 Gb genome size with 932 scaffolds ([~]732 Mb) anchored to 24 chromosomes that are available as a karyotype browser at www.nutrigroup-iats.org/seabreambrowser. Homology-based functional annotation, supported by RNA-seq transcripts, identified 55,423 actively transcribed genes corresponding to 21,275 unique descriptions with more than 55% of duplicated genes. The mobilome accounts for the 75% of the full genome size and it is mostly constituted by introns (599 Mb), whereas the rest is represented by low complexity repeats, RNA retrotransposons, DNA transposons and non-coding RNAs. This mobilome also contains a large number of chimeric/composite genes (i. e. loci presenting fragments or exons mostly surrounded by LINEs and Tc1/mariner DNA transposons), whose analysis revealed an enrichment in immune-related functions and processes. Analysis of synteny and gene phylogenies uncovered a high rate of species-specific duplications, resulting from recent independent duplications rather than from genome polyploidization (2.024 duplications per gene; 0.385 excluding gene expansions). These species-specific duplications were enriched in gene families functionally related to genome transposition, immune response and sensory responses. Additionally, transcriptional analysis of liver, skeletal muscle, intestine, gills and spleen supported a high number of functionally specialized paralogs under tissue-exclusive regulation. Altogether, these findings suggest a role of recent large-scale gene duplications coupled to tissue expression diversification in the evolution of gilthead sea bream genome during its successful adaptation to a changing and pathogen-rich environment. This issue also underscores a role of evolutionary routes for rapid increase of the gene repertoire in teleost fish that are independent of polyploidization. Since gilthead sea bream has a well-recognized plasticity, the current study will advance our understanding of fish biology and how organisms of this taxon interact with the environment.

genomics↗