Custom media formulation for swine; collaboration?

[anderson-fsep]

Hello,

I have been attempting to use micom to predict Salmonella colonization in the swine hindgut under different dietary contexts (control diet +/- prebiotic resistant starch) from fecal and cecal metagenomes. ~75% of the metagenome abundance maps to the AGORA database at genus level so I think translating these models to swine might have promise. However, I am having a hard time converting the attached dietary formulations into a custom media in micom - assuming there is enough data in the table to do this? I am wondering if someone can help me get started with this?

I am aware of the examples in the MICOM media repository but I think I am missing that first step of using vmh (or something else?) to generate the reaction-flux-metabolite table.

Further, how can resistant starch be added, as I dont see fibers like this in vmh? From Quinn-Bohmann et al,(https://www.nature.com/articles/s41564-024-01728-4), "Residual dietary fibre not easily digested, including resistant starch, dextrin and cellulose, was not removed from the medium during carbon removal. The amount of this residual fibre was scaled to the dilution factor of samples in each study before culturing. To simulate fibre supplementation, single-fibre additions were made to the medium, either pectin, inulin or fructo-oligosaccharide (1.0 mmol gDW−1 h−1 for pectin, 10.0 mmol gDW−1 h−1 for inulin and 100 mmol gDW−1 h−1 for fructo-oligosaccharide, based on carbon content reported for each)."

I am open to a more formal collaboration as well if someone is interested in exploring this new research angle with me.

Thanks!
Chris