Question about the steps of creating the models

[Mushahid2521]

Hi there,
Thanks a lot for creating these great resources. I am working on a project to build community models. Unfortunately, some of the species are not present in this repository. To be consistent, I wanted to use the same steps so that I can use your models along with mine.

May I know given a genome file, what are the tools and steps are followed to create these models. Which annotation tool and then followed by any media or gap filling before passing it to carveme?

Thanks a lot. Your help would be much appreciated.

[hellopeccat]

Hello @Mushahid2521 ,

I am a guest, and just occasionally read your issue. The original work of the publisher could be found here. In the sections titled Gene annotation, and Large-scale model reconstruction and community models, respectively, you will get the detailed statements.

But, more importantly, if you are working on modeling communities by FBA or flux sampling, I would like to remind you that this database of embl_gems is based on a universal biomass reaction which you will find formulated identically as follows in each xml file:

    <listOfReactants>
      <speciesReference species="M_10fthf_c" stoichiometry="0.000215957436615497" constant="true"/>
      <speciesReference species="M_ala__L_c" stoichiometry="0.497466186805283" constant="true"/>
      <speciesReference species="M_amet_c" stoichiometry="0.000215957436615497" constant="true"/>
      <speciesReference species="M_arg__L_c" stoichiometry="0.286450592337987" constant="true"/>
      <speciesReference species="M_asn__L_c" stoichiometry="0.233442241629366" constant="true"/>
      <speciesReference species="M_asp__L_c" stoichiometry="0.233442241629366" constant="true"/>
      <speciesReference species="M_atp_c" stoichiometry="52.4155146188655" constant="true"/>
      <speciesReference species="M_ca2_c" stoichiometry="0.00504062088602539" constant="true"/>
      <speciesReference species="M_cl_c" stoichiometry="0.00504062088602539" constant="true"/>
      <speciesReference species="M_coa_c" stoichiometry="0.000557809343006845" constant="true"/>
      <speciesReference species="M_cobalt2_c" stoichiometry="9.68418998275772e-05" constant="true"/>
      <speciesReference species="M_ctp_c" stoichiometry="0.129291683621802" constant="true"/>
      <speciesReference species="M_cu2_c" stoichiometry="0.000686609069777522" constant="true"/>
      <speciesReference species="M_cys__L_c" stoichiometry="0.0886878118620952" constant="true"/>
      <speciesReference species="M_datp_c" stoichiometry="0.0253396515088839" constant="true"/>
      <speciesReference species="M_dctp_c" stoichiometry="0.0261637760764165" constant="true"/>
      <speciesReference species="M_dgtp_c" stoichiometry="0.0261637760764165" constant="true"/>
      <speciesReference species="M_dttp_c" stoichiometry="0.0253396515088839" constant="true"/>
      <speciesReference species="M_fad_c" stoichiometry="0.000215957436615497" constant="true"/>
      <speciesReference species="M_fe2_c" stoichiometry="0.00650293357342181" constant="true"/>
      <speciesReference species="M_fe3_c" stoichiometry="0.00756141553853723" constant="true"/>
      <speciesReference species="M_gln__L_c" stoichiometry="0.254849143586252" constant="true"/>
      <speciesReference species="M_glu__L_c" stoichiometry="0.254849143586252" constant="true"/>
      <speciesReference species="M_gly_c" stoichiometry="0.593290278265672" constant="true"/>
      <speciesReference species="M_gtp_c" stoichiometry="0.208303052853126" constant="true"/>
      <speciesReference species="M_h2o_c" stoichiometry="47.0666420920129" constant="true"/>
      <speciesReference species="M_his__L_c" stoichiometry="0.0917460790586501" constant="true"/>
      <speciesReference species="M_ile__L_c" stoichiometry="0.281353803150062" constant="true"/>
      <speciesReference species="M_k_c" stoichiometry="0.189028609530443" constant="true"/>
      <speciesReference species="M_leu__L_c" stoichiometry="0.436302779712182" constant="true"/>
      <speciesReference species="M_lys__L_c" stoichiometry="0.332323631867312" constant="true"/>
      <speciesReference species="M_met__L_c" stoichiometry="0.14883244216901" constant="true"/>
      <speciesReference species="M_mg2_c" stoichiometry="0.00840103481004232" constant="true"/>
      <speciesReference species="M_mlthf_c" stoichiometry="0.000215957436615497" constant="true"/>
      <speciesReference species="M_mn2_c" stoichiometry="0.000669177527808559" constant="true"/>
      <speciesReference species="M_mql8_c" stoichiometry="9.68418998275772e-05" constant="true"/>
      <speciesReference species="M_nad_c" stoichiometry="0.00177317518584294" constant="true"/>
      <speciesReference species="M_nadp_c" stoichiometry="0.00043288329222927" constant="true"/>
      <speciesReference species="M_phe__L_c" stoichiometry="0.179414145715561" constant="true"/>
      <speciesReference species="M_pro__L_c" stoichiometry="0.214073861663851" constant="true"/>
      <speciesReference species="M_pydx5p_c" stoichiometry="0.000215957436615497" constant="true"/>
      <speciesReference species="M_ribflv_c" stoichiometry="0.000215957436615497" constant="true"/>
      <speciesReference species="M_ser__L_c" stoichiometry="0.208977072475925" constant="true"/>
      <speciesReference species="M_so4_c" stoichiometry="0.0042010016145203" constant="true"/>
      <speciesReference species="M_thf_c" stoichiometry="0.000215957436615497" constant="true"/>
      <speciesReference species="M_thmpp_c" stoichiometry="0.000215957436615497" constant="true"/>
      <speciesReference species="M_thr__L_c" stoichiometry="0.245675310415586" constant="true"/>
      <speciesReference species="M_trp__L_c" stoichiometry="0.0550478411189897" constant="true"/>
      <speciesReference species="M_tyr__L_c" stoichiometry="0.133541106186236" constant="true"/>
      <speciesReference species="M_uaagmda_c" stoichiometry="0.0968418998275772" constant="true"/>
      <speciesReference species="M_utp_c" stoichiometry="0.139553051327532" constant="true"/>
      <speciesReference species="M_val__L_c" stoichiometry="0.409798120148372" constant="true"/>
      <speciesReference species="M_zn2_c" stoichiometry="0.000330230878412038" constant="true"/>
    </listOfReactants>
    <listOfProducts>
      <speciesReference species="M_adp_c" stoichiometry="52.2462049569779" constant="true"/>
      <speciesReference species="M_h_c" stoichiometry="52.2462049569779" constant="true"/>
      <speciesReference species="M_pi_c" stoichiometry="52.2420039553634" constant="true"/>
      <speciesReference species="M_ppi_c" stoichiometry="0.749462368022615" constant="true"/>
    </listOfProducts>

If the biomass components of your microbial communities are known, you had better substitute the universal biomass reaction. Since as a key phenotype and the sink of metabolic network, the biomass reaction will determine the flux distribution from a overall level.

I have also been working on GEMs reconstruction of microbial communities, feel it free to discuss and share your opinions with me.
Best wishes.