TbasCO: trait-based comparative ‘omics identifies ecosystem-level and niche-differentiating adaptations of an engineered microbiome
E.A. McDaniel et al. "TbasCO: trait-based comparative ‘omics identifies ecosystem-level and niche-differentiating adaptations of an engineered microbiome" ISME Communications 2 (2022) [DOI: 10.1038/s43705-022-00189-2]
A grand challenge in microbial ecology is disentangling the traits of individual populations within complex communities. Various cultivation-independent approaches have been used to infer traits based on the presence of marker genes. However, marker genes are not linked to traits with complete fidelity, nor do they capture important attributes, such as the timing of gene expression or coordination among traits. To address this, we present an approach for assessing the trait landscape of microbial communities by statistically defining a trait attribute as a shared transcriptional pattern across multiple organisms. Leveraging the KEGG pathway database as a trait library and the Enhanced Biological Phosphorus Removal (EBPR) model microbial ecosystem, we demonstrate that a majority (65%) of traits present in 10 or more genomes have niche-differentiating expression attributes. For example, while many genomes containing high-affinity phosphorus transporter pstABCS display a canonical attribute (e.g. up-regulation under phosphorus starvation), we identified another attribute shared by many genomes where transcription was highest under high phosphorus conditions. Taken together, we provide a novel framework for unravelling the functional dynamics of uncultivated microorganisms by assigning trait-attributes through genome-resolved time-series metatranscriptomics.
All supplementary files including functional annotations, transcriptome count files, and two reassembled Accumulibacter genomes are available on figshare. All 64 genomes have been deposited in NCBI at Bioproject PRJNA714686. The three metagenomes and six metatranscriptomes used in this study are available on the JGI/IMG at accession codes 3300026302, 3300026286, 3300009517, and 3300002341-46, respectively. All code for performing metagenomic assembly, binning, and annotation can be found on GitHub. The TbasCO method has been implemented as a reproducible R package and can be accessed on GitHub.