Species-specific transcriptomic network inference of interspecies interactions

Abstract

The advent of high-throughput 'omics approaches coupled with computational analyses to reconstruct individual genomes from metagenomes provides a basis for species-resolved functional studies. Here, a mutual information approach was applied to build a gene association network of a commensal consortium, in which a unicellular cyanobacterium Thermosynechococcus elongatus BP1 supported the heterotrophic growth of Meiothermus ruber strain A. Specifically, we used the context likelihood of relatedness (CLR) algorithm to generate a gene association network from 25 transcriptomic datasets representing distinct growth conditions. The resulting interspecies network revealed a number of linkages between genes in each species. While many of the linkages were supported by the existing knowledge of phototroph-heterotroph interactions and the metabolism of these two species several new interactions were inferred as well. These include linkages between amino acid synthesis and uptake genes, as well as carbohydrate and vitamin metabolism, terpenoid metabolism and cell adhesion genes. Further topological examination and functional analysis of specific gene associations suggested that the interactions are likely to center around the exchange of energetically costly metabolites between T. elongatus and M. ruber. Both the approach and conclusions derived from this work are widely applicable to microbial communities for identification of the interactions between species and characterization of community functioning as a whole.

Plant–necrotroph co-transcriptome networks illuminate a metabolic battlefield

“…Co-transcriptomic approaches whereby the host and pathogen transcriptomes are simultaneously analyzed provide the ability to systematically map the cross-kingdom communication between plant hosts and their pathogens, both for individual genes and gene co-expression network (GCN) levels (Stuart et al, 2003; Musungu et al, 2016; Zhang et al, 2017; Lanver et al, 2018; McClure et al, 2018). Recent advances have enabled the measurement of pathogen in planta transcriptome.…”

The Transcriptome of Verticillium dahliae Responds Differentially Depending on the Disease Susceptibility Level of the Olive (Olea europaea L.) Cultivar

“…However, these studies are difficult because of the complexity for accurate discrimination between transcripts from the host and the pathogen. Therefore, these approaches are not frequent and have mostly focused on individual genes or gene co-expression networks e.g., [44,45,46,47]. Previously, we conducted a study in which olive (cv.…”

Reconciling Ecological and Engineering Design Principles for Building Microbiomes

“…There are two common approaches—within the current state of the science—for developing model microbial communities: top-down selection of natural microbiomes toward representative consortia with reduced complexity (7) and bottom-up construction of consortia, which are predesigned assemblages based on hypotheses or specific engineering design principles (8–10). These approaches have been discussed and compared in a number of review and perspective articles (2–4, 11) and hence will not be covered in more detail here.…”