Add (optionally) information on butyrate producers to rowData in importing the taxonomic abundances

[antagomir]

The following taxa are identified as key butyrate producers (reference: Kullberg et al. 2024).
"Butyricimonas", "Odoribacter", "Alistipes", "Eubacterium", "Anaerostipes","Butyrivibrio", "Coprococcus_2", "Coprococcus_3", "Roseburia", "Shuttleworthia", "Butyricicoccus", "Faecalibacterium", "Flavonifractor", "Pseudoflavonifractor", "Oscillibacter", "Ruminococcus_2", "Subdoligranulum"

These can be mapped to the given taxonomy (manually) and could be provided as an optional rowData field with the metaphlan, GG2 etc importers, or as an additional post-import enrichment function. This can be useful for some data interpretation and analyses.

On the other hand, such manual listing will remain controversial and a more customized utility package might be better for such purpose. However, mia could provide a suitable initial home for testing also this kind approaches for data enrichment.

Reference:

Association between butyrate-producing gut bacteria and the risk of infectious disease hospitalisation: Results from two observational, population-based microbiome studies
Kullberg R, Wikki I, Haak B, Kauko A, Galenkamp H, Peters-Sengers H, Butler J, Havulinna A, Palmu J, McDonald D, Benchraka C, Abdel-Aziz M, Prins M, Maitland van der Zee A, Born B, Jousilahti P, Vos W, Salomaa V, Knight R, Lahti L, Nieuwdorp M, Niiranen T & Wiersinga W.
The Lancet Microbe 2024
https://doi.org/10.1016/S2666-5247(24)00079-X

[TuomasBorman]

I think mia is not the best place for this because mia is more about tools, not this kind of datasets. Would microbiomeDataSets be more suitable, for instance?

[antagomir]

Yes, possibly. This would take a more systematic approach to develop a resource that has a collection standardized annotations for features and it could be used to enrich data from standard pipelines on the fly.