A - Papers appearing in refereed journals
Gardiner, L., Marshall, M., Reusch, K., Dearden, C., Birmingham, M., Carrieri, A. P., Pyzer-Knapp, E. O., Krishna, R. and Neal, A. L. 2024. DGCNN approach links metagenome-derived taxon and functional information providing insight into global soil organic carbon. NPJ Biofilms Microbiomes. 10, p. 113. https://doi.org/10.1038/s41522-024-00583-9
Authors | Gardiner, L., Marshall, M., Reusch, K., Dearden, C., Birmingham, M., Carrieri, A. P., Pyzer-Knapp, E. O., Krishna, R. and Neal, A. L. |
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Abstract | Metagenomics can provide insight into the microbial taxa present in a sample and, through gene identification, the functional potential of the community. However, taxonomic and functional information are typically considered separately in downstream analyses. We develop interpretable machine learning (ML) approaches for modelling metagenomic data, combining the biological representation of species with their associated genetically encoded functions within models. We apply our methods to investigate soil organic carbon (SOC) stocks. First, we combine a diverse global set of soil microbiome samples with environmental data, improving the predictive performance of classic ML and providing new insights into the role of soil microbiomes in global carbon cycling. Our network analysis of predictive taxa identified by classical ML models provides context for their ecological |
Year of Publication | 2024 |
Journal | NPJ Biofilms Microbiomes |
Journal citation | 10, p. 113 |
Digital Object Identifier (DOI) | https://doi.org/10.1038/s41522-024-00583-9 |
Open access | Published as ‘gold’ (paid) open access |
Funder | Biotechnology and Biological Sciences Research Council |
Funder project or code | Growing Health [ISP] |
Growing Health (WP2) - bio-inspired solutions for healthier agroecosystems: Understanding soil environments | |
Publisher's version | |
Output status | Published |
Publication dates | |
Online | 26 Oct 2024 |
Publication process dates | |
Accepted | 11 Oct 2024 |
Permalink - https://repository.rothamsted.ac.uk/item/9922q/dgcnn-approach-links-metagenome-derived-taxon-and-functional-information-providing-insight-into-global-soil-organic-carbon