Get binary azo-rhodo working with a carbon source that only rhodo grows on

[djinnome]

for example, xylose, but you can use any biolog carbon compound that is + for rhodo and - for azo.

[mcnaughtonadm]

Using Xylose as the carbon source, we can grow the binary between azo and rhodo.

compartments	abundance	growth_rate	reactions	metabolites
Azotobacter	0.5	0.371855	2469	2003
Rhodosporidium	0.5	1.037279	2398	2051
medium	NaN	NaN	449	449

The default media provides glc__D_m at a flux value of 5 which when optimizing the binary, doesn't lead to growth. When adding xyl__D_m at a flux of 5, there is growth in both organisms. When using just xyl__D_m at a flux value of 5, there is not community growth. When using xyl__D_m with a flux value of 10, there is community growth. Seems like there is not enough carbon in the model to grow under the model provided 'Default'. Should we make modifications to the model until we can grow with xyl__D_m using a flux value of 5, or consider growing with 10 a success of binary growth?

[djinnome]

Binary growth where only Rhodo can consume an external carbon source is the goal. Can you confirm that Azo is not consuming xyl__D_m and can you tell me what internal carbon source(s) Azo is consuming?

[mcnaughtonadm]

In this instance with 10 xyl__D_e, it is the sole carbon source (there are some minor trna SRC reactions acting as uptake but 97.72% of carbon is provided by xylose). All of that is being used by Rhodo so Azo is not consuming it.

Internally, just by briefly viewing the fluxes (more may pop up with a visualization), Azo is importing EX_glcn_e (D-gluconate) from Rhodosporidium's export (table below).

Organism	Flux
Azotobacter	-11.84127256
Rhodosporidium	11.84127256

[djinnome]

Congratulations, this counts as success! As a bonus round, do we know if Rhodo actually excretes gluconate under xylose conditions? And if so, does Azo really eat it? i.e. can we check the Azo Biolog and the Rhodo-Cyano metabolite exchange data to see if gluconate is in there?

[djinnome]

Lastly, do we know if Cyano is capable of secreting xylose if we were to replace the engineered sucrose transporter with a xylose transporter?

[djinnome]

@PBohutskyi ?