######## Basic information of the symbiotic microorganisms associated with the sponge Stylissa sp. ######## ## Taxonomic classification of the eight microbial species, their abbreviations (i.e., OTU + a figure), and the functional population they represent: # OTU1: Spongiicolonus versatilis -- SOB # OTU2: Parasynechococcus marinus -- photosymbiont # OTU3: Deltaporibacter stylissae -- Denitrifier # OTU4: Spongiihabitans thiooxidans -- SOB # OTU5: Gammaporibacter thiotrophicus -- SOB # OTU6: Nitrospongiibacter stylissae -- NOB # OTU7: Oxydemutator thiolithooxidans -- SOB # OTU8: Cenoporarchaeum stylissae -- AOA ####### Command lines of using BacArena to conduct network simulations ####### # 1. To simulate an in silico growth test for a single microbial species, here is an example using the model of NOB: ~/STY8/Cmds_for_running_R_scripts/Cmds_Single-species_simulations/Cmds_for_Rscript_BacArena_SingleSpecies__simuDiet_optparse_pFBA_ka.sh # 2. To simulate a network of the two-species microbial consortium, which includes both the NOB and AOA models, execute the following command line: ~/STY8/Cmds_for_running_R_scripts/Cmds_2-species_network/Cmds_for_Rscript_BacArena_otu6n8__simuDiet_optparse_FBA_ka.sh # 3. To simulate a network of the three-species microbial consortium, which includes the NOB, AOA and photosymbiont models, run the following command line: ~/STY8/Cmds_for_running_R_scripts/Cmds_3-species_network/Cmds_for_Rscript_BacArena_otu2n6n8__simuDiet_optparse_FBA_ka.sh # 4. To simulate a network of the eight-species microbiome, here is an example using hypotaurine as the sole organic carbon at a concentration of 0.2 mM: ~/STY8/Cmds_for_running_R_scripts/Cmds_8-species_network/Cmds_for_Rscript_BacArena_8species__simuDiet_optparse_pFBA_ka.sh ######## Citation ####### Shan Zhang, Weizhi Song, Geogios Marinos, Silvio Waschina, Johannes Zimmermann, Christoph Kaleta, Torsten Thomas. (2024) Genome-scale metabolic modelling reveals interactions and key roles of symbiont clades in a sponge holobiont.