simulatePairwiseInteractions not returning expected values?

[BooksAreMyChoiceWeapon]

I've been trying to simulate bacteria pairings using GapSeq models my team created in the lab. When I pair up models and simulate interactions using simulatePairwiseInteractions, they grow like crazy when I don't include a diet, but when I use a diet, half of them don't grow - even by themselves.

This is output of a program where I randomly pick a few bacteria, pair them up, and simulate the interactions.
With diet:

Without diet:

I thought that maybe the diet I was using was 'killing' the bacteria, so I decided to run each bacterium in the set through FBA by itself, both with and without the diet, and got completely different growth values as output.

Some of the singleGrowth values for the paired bacteria match their FBA output under the diet (such as H29) but most of them don't. Is there a reason for this? Do I need to fix something?

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• Tried to solve the issue on my own
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[almut-heinken]

Hello @BooksAreMyChoiceWeapon ,
what diet are you using exactly? Please keep in mind that the names of the exchange reactions change for the pairwise models so you need to adjust for that.
Best,
Almut

[BooksAreMyChoiceWeapon]

I used a custom diet I developed from a paper I found - I called it the Pirate Diet because it's for marine bacteria.

I'll attach a copy of the diet here:
NewDMMPirateDiet.xlsx

I have it set in the format for pairwise models with the [u] at the end, and I added a few lines for the single FBA analysis that tweaked the names in the list so they ended in '_e0' instead.

The only thing I can think of is the Molybdenum ion? None of the models I'm working with use it apparently - I keep getting messages about it. I wouldn't think it would mess up the pairwise models though when the single FBA analysis runs fine?

[almut-heinken]

Hello @BooksAreMyChoiceWeapon
looks good at first glance so I cannot say for sure. It seems like only ATL01 and ATL20 are non-growing. Could you try looking at the reduced costs/shadow prices when growing the pairwise models to see if that gives you an idea?

[BooksAreMyChoiceWeapon]

How exactly would I go about doing that? Sorry I'm kinda new to the toolbox.

[rmtfleming]

Hi BooksAreMyChoiceWeapon, what is your name, research group and institutional affiliation? Regards, Ronan

…

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-- -- Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D. ---------------------------------------------------------------------------- Associate Professor, School of Medicine, National University of Ireland, Galway. & Assistant Professor, Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University. https://www.universiteitleiden.nl/en/staffmembers/ronan-fleming & H2020 Project Coordinator, Systems Medicine of Mitochondrial Parkinson’s Disease, http://sysmedpd.eu ---------------------------------------------------------------------------- Peer-reviewed publications: https://goo.gl/FZPG23 Mobile: +353 852 109 806 Skype: ronan.fleming ---------------------------------------------------------------------------- (This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.)

[almut-heinken]

How exactly would I go about doing that? Sorry I'm kinda new to the toolbox.

@BooksAreMyChoiceWeapon You need to run an FBA on the pairwise model and then inspect the "y" (corresponding to metabolites) and "w" (corresponding to reactions) fields in the FBA solution.