q2-fungal-traits: a QIIME 2 plugin for trait-based analysis of fungal microbiome data

Community Contributions Plugins
1

Hi everyone,

We are excited to share a new plugin, q2-fungal-traits, for automated integration of fungal taxonomy derived from marker-gene amplicon (e.g., ITS, other regions) or shotgun metagenomic sequencing data with ecological and functional trait information compiled from published fungal trait datasets.

The plugin provides an annotate action that generates a metadata table containing fungal trait annotations and spore size estimates based on fungal taxonomic assignments. These annotations include information on key fungal phenotypes and traits, such as morphology and lifestyle, which can be useful for ecological inference and detection of potential contaminants in fungal microbiome datasets. This can be integrated directly into standard QIIME 2 workflows, for example to filter features based on certain trait criteria.

Documentation and usage instructions are available at:
https://library.qiime2.org/plugins/bokulich-lab/q2-fungal-traits.

To learn more about q2-fungal-traits, benefits of trait-based mycobiome analyses, and potential use cases, see our bioRxiv preprint:

Lavrinienko, A., Risch, V., Tang, C., Meyer, A., Flörl, L., Bokulich, N.A. 2026. Ecological inference and contaminant detection from fungal microbiome data with q2-fungal-traits. bioRxiv. https://doi.org/10.64898/2026.06.17.732913

If you have any questions, feedback, or bug reports, please open a new topic on the QIIME 2 Forum. We hope q2-fungal-traits will be a useful addition to your fungal microbiome analysis workflows :mushroom:

Thanks,
Anton

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Hi @alavrinienko

Thank you very much for the q2-fungal-trails plugin! It will be very helpful in environmental studies, and the first analyses within the qiime2 environment look very promising for downstream analyses and result interpretation.

The output of q2-fungal-traits is an 'ImmutableMetadata' type. I am wondering if (and how) these metadata could be used for subsequent visualization steps within q2? We often compare sample groups for differential abundance of fungal taxa, and I would be interested to learn how I can use the fungal-traits metadata artifact to visualize fungal traits (at least a few selected ones) within identified differentially-abundant taxa. I am thinking about heatmaps, or bubble plots (something like the bubble plot shown on the online instructions of FAPROTAX for bacterial functions). Do you know other visualization possibilies in q2?

I am aware, that q2-fungal-traits annotates the taxonomy artifact without collapsing the identified taxa under specific traits, and thus differs from FAPROTAX. Could the original ASV abundance table in combination with fungal traits output be used to produce some kind of visualization? Perhaps in combination with q2-feature-table tabulate-feature-frequencies? I also found qiime sample-classifier heatmap with the parameters --m-feature-metadata-file and --m-feature-metadata-columnas possible input options; do you know if fungal-traits columns of the ImmutableMetadata could be used here?

Best regards

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Hi @arwqiime,

Thanks for your feedback - glad to hear you find the q2-fungal-trails plugin useful in your research!

Good question re options for downstream visualization. I have not tried visualizing the resulting annotations directly in QIIME 2 myself, but in principal this output can be used anywhere that a metadata file can be used in QIIME 2.

I would suggest looking into the q2-metadata plugin (How to merge metadata - Using QIIME 2) to explore options for merging fungal trait annotations optimally with other relevant feature- or sample-level metadata, depending on what you want to visualize. You could also explore filtering options to focus on differentially abundant taxa.

Since you mentioned heatmaps, I would also check out the visualization options available through the q2-vizard plugin (QIIME 2 Library). Alternatively, you can always export the annotations as a metadata TSV file and use them for plotting outside QIIME 2.

I hope that helps!

Anton

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