[AGORA 1.03] Lower bound for "demand for Biotin" sink reaction is set to 0.1 on some models

[nigiord]

Hi and thank you for providing AGORA,

I noticed some strange interactions with biotin (btn) for some of the models provided in AGORA 1.03, which made me investigate. There are 140 models in AGORA 1.03 that contain the following sink reaction for biotin:

<reaction metaid="R_DM_btn" id="R_DM_btn" name="Demand for biotin" reversible="false" fast="false" fbc:lowerFluxBound="…" fbc:upperFluxBound="…">

of which:

• 136 have lower and upper bounds of 0 and 1000
• 4 have lower and upper bounds of 0.1 and 1000

Those 4 models are:

Clostridium_sporogenes_ATCC_15579.xml Faecalibacterium_prausnitzii_M21_2.xml Faecalibacterium_prausnitzii_SL3_3.xml Lactobacillus_fermentum_ATCC_14931.xml

Technically, this lower bound on a sink reaction means that the model cannot grow without having access to at least 0.1 mmol/human/day of biotin (either exchanged from the medium, or produced internally). I initially thought this was because biotin was reported to be an essential metabolite for those 4 bacteria, but when looking at the Supplementary Table provided, there are 32 bacteria for which biotin is noted as essential, and Lactobacillus_fermentum_ATCC_14931 is not even one of them. Apparently such a lower bound was not present in AGORA 1.02.

What's the reason for having a 0.1 mmol/human/day lower bound on this sink reaction in those specific 4 models?

Best regards, −Nils