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.
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Acknowledgements
The authors wish to acknowledge Drs. Margie Romine, William Nelson, and Jim Fredrickson for help with the functional genome annotation and manuscript. PNNL is operated for the DOE by Battelle Memorial Institute under Contract DE-AC05-76RLO 1830. The research was supported by the Genomic Science Program (GSP), Office of Biological and Environmental Research (BER), U.S. Department of Energy (DOE), and is a contribution of the PNNL Foundational Scientific Focus Area (FSFA). A significant portion of the research was performed using the Environmental Molecular Sciences Laboratory (EMSL), a national scientific user facility sponsored by DOE BER and located at PNNL. HCB is grateful for the support of the Linus Pauling Distinguished Postdoctoral Fellowship program at PNNL.
Author contributions
RSM performed the experiments, analyzed the data and wrote the manuscript, CCO analyzed the data and contributed to the manuscript preparation, EAH contributed to the experiments, MC contributed to the experiments, HCB contributed to the experiments and manuscript preparation, JM contributed to the experimental design and manuscript preparation, ASB developed the project concept, contributed to the experimental design, and wrote the manuscript.
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41396_2018_145_MOESM10_ESM.xlsx
Supplementary Table 5: Functional enrichment of T. elongatus genes linked to uncharacterized M. ruber genes SY28_RS04830 and SY28_RS05160
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McClure, R.S., Overall, C.C., Hill, E.A. et al. Species-specific transcriptomic network inference of interspecies interactions. ISME J 12, 2011–2023 (2018). https://doi.org/10.1038/s41396-018-0145-6
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DOI: https://doi.org/10.1038/s41396-018-0145-6
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