# AGORA reconstructions version 1.01, published online 20.01.17

In the previously distributed version of AGORA, 17 models could not grow if flux through all oxygen-containing reactions was blocked. In order to enable anaerobic growth for these reconstructions, a gap-filling was performed that enabled the production of essential biomass precursors while bypassing oxygen-containing reactions. Furthermore, we replaced several reactions unlikely to be reversible with the irreversible versions of these reactions.

Moreover, the constraints implemented on the exchange reactions in the distributed version of AGORA were inconsistent across the 773 reconstructions. We now provide the AGORA reconstructions in SBML format as models simulating three different conditions: (1) AGORA reconstructions (AGORA 1.01 - Reconstructions), (2) AGORA with Western diet (anaerobic) constraints implemented as described in Supplementary Table 12 (AGORA 1.01 - Western Diet constrains), (3) AGORA with High fiber diet (anaerobic) constraints implemented as described in Supplementary Table 12 (AGORA 1.01 - High fiber diet constrains).

We thank Parizad Babaei, Saeed Shoaie, Boyang Ji and Jens Nielsen for pointing out these oversights.

| VMH ID of added gap-filled reactions	| # reconstructions |
|---------------------------------------|-------------------|
| 2DMMQ8abc	| 1 |
| DMATT	| 4 |
| DMPPS	| 5 |
| DMQMT	| 1 |
| EX_2dmmq8(e)	| 1 |
| EX_pheme(e)| 2 |
| EX_q8(e) | 10 |
| EX_so4(e) | 1 |
| EX_thm(e) | 2 |
| GRTT | 4 |
| HEMEti | 2 |
| OMBZLM | 1 |
| OMMBLHX3 | 1 |
| OMPHHX3 | 1 |
| OPHHX3 | 1 |
| Q8abc | 10 |
| SO4t2 | 1 |
| THMabc | 2 |
| TMDPK | 1 |
[Table 1. Summary of gap-filled reactions added to enable biomass production while flux through internal oxygen-containing reactions is blocked (17 reconstructions in total).]

| VMH ID of removed reactions | # reconstructions |
|-----------------------------|-------------------|
| 2OMMBOX | 5 |
| 2OMPHH | 5 |
| 4HBADH | 1 |
| 4HBZt2 | 1 |
| CHRPL | 6 |
| DDCAt | 2 |
| DMQMT2 | 5 |
| EX_ddca(e) | 2 |
| X_ttdca(e) | 2 |
| FA140ACPH | 2 |
| FA161ACPH | 2 |
| FAO11 | 2 |
| FAS161ACP | 2 |
| FERO | 3 |
| FRDPS | 15 |
| H2SO | 1 |
| HBZOPT | 7 |
| HETT | 1 |
| HEXTT | 3 |
| IPFPHS | 3 |
| KAS16 | 2 |
| LANOSTt | 15 |
| OHPHM | 8 |
| OPHBDC | 7 |
| OPHHX | 10 |
| PPPH | 1 |
| SQLE | 3 |
| SQLErev | 12 |
| SSQEPXS | 15 |
| TMDSf2 | 2 |
| TTDCAt2 | 2 |
| URFGTT | 4 |
| VNDH-2 | 1 |
[Table 2: Summary of reactions not supported by genome annotation that were gap-filled by Model SEED and deleted (17 reconstructions in total). The reason for their deletion was that they were no longer required for biomass production due to the changes described in Table 1.]

| VMH ID of replaced reactions |VMH ID of irreversible replacement reactions |# reconstructions | Notes |
|------------------------------|---------------------------------------------|------------------|-------|
| ASPK |	ASPKi | 304 | Unlikely to be reversible (may cause unlikely ATP production or carbon fixation). |
| D4DGCD |	D4DGCDi | 3 | Caused futile cycles in certain reconstructions. |
| DDGLKr |	DDGLK | 351 | Unlikely to be reversible (may cause unlikely ATP production or carbon fixation). |
| G3PD8 |	G3PD8i | 1 | Caused futile cycles in certain reconstructions. |
| GHMT2r |	GHMT2 | 6 | Caused futile cycles in certain reconstructions. |
| GLYC3Pt |	GLYC3Pti | 2 | Caused futile cycles in certain reconstructions. |
| GUAt2r |	GUAt2 | 193 | Unlikely to be reversible (may cause unlikely ATP production or carbon fixation). |
| METATr |	METAT |	772 | Unlikely to be reversible (may cause unlikely ATP production or carbon fixation). |
| NMNATr |	NMNAT |	481 | Unlikely to be reversible (may cause unlikely ATP production or carbon fixation). |
| OCOAT1r |	OCOAT1 | 11 | Caused futile cycles in certain reconstructions. |
| PYDXKr |	PYDXK |	680 | Unlikely to be reversible (may cause unlikely ATP production or carbon fixation). |
| r0318 |	r0318i | 1 | Caused futile cycles in certain reconstructions. |
| r0556c |	r0556ci | 34 | Caused futile cycles in certain reconstructions. |
| RBK_Dr |	RBK_D |	381 | Unlikely to be reversible (may cause unlikely ATP production or carbon fixation). |
| TARCGLYL |	TARCGLYLi | 18 | Caused futile cycles in certain reconstructions. |
| TMKr |	TMK |	171 | Unlikely to be reversible (may cause unlikely ATP production or carbon fixation). |
| TMPKr |	TMPK | 504 | Unlikely to be reversible (may cause unlikely ATP production or carbon fixation). |
| TRPAS2 |	TRPAS2i | 1 | Caused futile cycles in certain reconstructions. |
| XYLKr |	XYLK | 209 | Unlikely to be reversible (may cause unlikely ATP production or carbon fixation). |
[Table 3: Summary of reactions replaced by irreversible versions to remove thermodynamically infeasible constraints from the reconstructions (773 reconstructions in total).]