Report
Ranking Biological Features in Soil-Based Microbial Multi-Omics Data with Integration Modeling
Vol.PNNL-38772
Pacific Northwest National Laboratory
12/31/2025
DOI: 10.2172/3012132
Abstract
Distinguishing the most important features (e.g. proteins, metabolites, etc.) per group (e.g. control and treatment) is a critical challenge in feature-rich multi-omics experiments, especially in soil data. Traditional feature identification and ranking approaches, such as differential expression, are based on single omics and thus not directly translatable to multi-omics experiments. Here, 5 multi-omics integration models (DIABLO, JACA, MOFA, MultiMLP, and SLIDE) that were not explicitly built for soil data applications were tested using a soil-based multi-omics experiment. The data were obtained from an experimental setup of an autoclaved soil system inoculated with 8 bacteria and using chitin as the carbon source and including samples collected at 0- (control), 4-, 8-, and 12-weeks post-inoculation. The omics data included metaproteomics, 16S rRNA sequencing, and LC-MS/MS metabolomics (in positive and negative mode). Each multi-omics integration model was implemented, and top features were compared to differential univariate statistics per omic type, demonstrating that integration approaches cut the potential number of top features from 2957 identified by differential statistics to 13-224 (a 99.6% to 92.4% reduction). Interestingly, most top features across integration models were not shared; though, scaling and averaging ranks across models shared similar patterns. This work highlights the usefulness of multi-omics integration models in soil-based microbial studies and the power of using multiple integration models together to interpret results.
Details
- Title: Subtitle
- Ranking Biological Features in Soil-Based Microbial Multi-Omics Data with Integration Modeling
- Creators
- David J. Degnan - Pacific Northwest National LaboratoryRyan S. McClure - Pacific Northwest National LaboratoryDaniel M. Claborne - Pacific Northwest National LaboratoryLisa M. Bramer - Pacific Northwest National LaboratoryJavier E. Flores - Pacific Northwest National Laboratory
- Resource Type
- Report
- Publication Details
- Vol.PNNL-38772
- DOI
- 10.2172/3012132
- Publisher
- Pacific Northwest National Laboratory; Richland, Washington
- Number of pages
- ii, 18 pages
- Language
- English
- Date published
- 12/31/2025
- Academic Unit
- Biostatistics
- Record Identifier
- 9985121483202771
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