Is it possible to predict auxotrophies from metabolic models generated by CarveMe?

[ilnamkang]

Hi,

I'd like to first note that I'm a nearly complete novice in metabolic modeling and systems biology

I'm interested in microbial auxotrophy, and I want to predict auxotrophies using only genome sequences in a rather scalable way.

Is it possible to predict auxotrophies from metabolic models generated by CarveMe?

If it is possible, are there any publicly available programs or protocols?

I've read your recent paper published in Nature Ecology & Evolution.

https://doi.org/10.1038/s41559-020-01353-4 Machado D, et al. 2021. Polarization of microbial communities between competitive and cooperative metabolism. Nature Ecology & Evolution 5:195-203.

According to this paper, metabolic models generated by CarveMe seem to have been used to predict (calculate) amino acid auxotrophies of numerous reference species. But, it's difficult for me to find detailed information about how this prediction has been performed.

Thank you.

Ilnam

[cdanielmachado]

Hi,

You can use this code: https://github.com/cdanielmachado/reframed/blob/master/reframed/cobra/auxotrophy.py

I hope this helps.

[ilnamkang]

Hi,

Thank you for a quick reply.

I'll give it a try.