Interpret core biological functions#
A functional profile helps ask what a microbial community can do, and which of those capabilities have protein evidence. A useful starting panel separates cellular housekeeping, functions common in the sampled ecosystem, and specialised functions. These are interpretation categories, not a universal list of genes required in every organism.
A starting panel for gut metaproteomics#
| Panel | Examples | Interpretation |
|---|---|---|
| Information processing | Translation/ribosomes, transcription, DNA replication and repair | Cellular maintenance and growth machinery |
| Central metabolism and energy | Central carbon reactions, ATP-generating machinery | Conserved biochemical processes; routes differ between organisms |
| Building blocks and cofactors | Amino-acid, nucleotide, vitamin and cofactor metabolism | Biosynthesis and salvage; auxotrophy and cross-feeding matter |
| Protein and cell maintenance | Protein folding/turnover, membrane and envelope processes | Cellular upkeep; not every component is universally essential |
| Gut ecosystem functions | Glycan utilisation, fermentation and short-chain-fatty-acid pathways | Functions distributed across community members; a different organism can provide the same reaction |
| Specialised functions | Selected xenobiotic transformations or other niche-specific pathways | Show a stated reference and biological rationale; do not label every non-core annotation as novel |
This is a proposed reporting panel, not a completed automated KO-to-core mapping. The initial labels follow the distinction between the minimal gut bacterial genome and the community metagenome in Qin et al. (2010). The expanded Human Microbiome Project distinguishes broadly distributed pathways from human-associated and body-site-enriched functions; its reported core depends on a specified population and detection rule. Lloyd-Price et al. (2017).
Keep three questions separate#
- Reference classification: is this a recognised housekeeping or ecosystem function?
- Observed prevalence: in how many eligible specimens was there evidence here?
- Molecular support: was the candidate selected by de novo, metaG, metaT or another declared source, and was it subsequently identified by MS?
Warning
Do not transfer a DNA prevalence threshold directly to proteomic detection. Undetected protein evidence does not establish biological absence. A KO hit does not establish a complete pathway or metabolic flux. Pathway/module completion requires the relevant alternative and required reactions to be evaluated. See the KEGG module definitions.
For paired multiomics, compare the same specimen and reference definitions, retain unannotated signal, and keep DNA potential, RNA evidence and measured protein quantities distinct. A newly selected FASTA member is not automatically a newly identified function. Demonstrating gains needs the paired baseline search too.