Environment files include lists of metabolites in their KEGG accessions. Each environment in a separate line. First string is environment's
id followed by metabolite accessions that are space-delimited. An example file is provided in the website including a minimal
environment with carbon and nitrogen sources (glucose and ammonium; Env_1 in the example file in the website), carbon source only (Env_2), nitrogen source only (Env_3),
and a rich environment with multiple carbons, co factors, amino acids and additional compounds (Env_4).
In addition, below we provide examples for four representations of environments including artificial defined growth media (M9; ATCC medium 2511 ) and natural compiled based
on experimental analyses (Tomato_Phloem_Env; [2,3,4,5,6]) or computational based proxy (Cucumber_Root_Env, Bulk_Soil_Env; ).
Please cite Tal, O.; Selvaraj, G.; Medina, S.; Ofaim, S.; Freilich, S. NetMet: A Network-Based Tool for Predicting Metabolic Capacities of Microbial Species and their Interactions. Microorganisms 2020, 8, 840.
1. American Type Culture Collection medium 2511: https://www.atcc.org/~/media/B3590BBD1DF74203B0E8F0890ECF974F.ashx
2. Valle EM, Boggio SB, Heldt HW. Free amino acid composition of phloem sap and growing fruit of Lycopersicon esculentum. Plant Cell Physiol. 1998, 39:458-461
3. Luis G, Hernández C, Rubio C, González-Weller D, Gutiérrez Á, Revert C, Hardisson A. Trace elements and toxic metals in intensively produced tomatoes (Lycopersicon esculentum). Nutr Hosp. 2012, 27:1605-1609. doi: 10.3305/nh.2012.27.5.5944. PMID: 23478712.
4. Osorio S.; Ruan Y.-L.; Fernie A.R. An update on source-to-sink carbon partitioning in tomato. Front Plant Sci 2014, 5, 516-516, doi:10.3389/fpls.2014.00516
5. Alfocea, F.P.; Balibrea, M.E.; Alarcón, J.J.; Bolarín, M.C. Composition of Xylem and Phloem Exudates in Relation to the Salt-tolerance of Domestic and Wild Tomato Species. J. Plant Physiol. 2000, 156, 367-374, doi:https://doi.org/10.1016/S0176-1617(00)80075-9
6. Wolterbeek, H.T.; Willemse, P.C.M.; Van Die, J. Phloem and xylem import of water and solutes in tomato fruits. Acta Bot. Neerl. 1987, 36, 295-306, doi:10.1111/j.1438-8677.1987.tb02008.x
7. Ofaim S, Ofek-Lalzar M, Sela N, Jinag J, Kashi Y, Minz D, et al. Analysis of microbial functions in the rhizosphere using a metabolic-network based framework for metagenomics interpretation. Front. Microbiol. 2017,8:1606
NetMet is a tool for predicting metabolic performances of microorganisms and their corresponding combinations in
user-defined environments. The algorithm takes as input lists of: (i) Genome file: lists of species-specific
enzymatic reactions (EC numbers) (ii) Environment File: relevant metabolic environments The algorithm
generates as output lists of: (i) compounds that individual species can produce in each given environment
(ii) compounds that are predicted to be produced through complementary interactions NetMet can run on
single-species or interaction mode. In 'Single-species mode' prediction of metabolic capacities are made based
on individual species' network in the given environment(s). 'Interaction mode' is an extension of the
single-species mode, providing a list of metabolites that are produced through exchange reactions between
pair-wise combinations of given species. Such metabolites are termed 'complementary metabolites' and are defined
as such that are formed by species combinations but not by the corresponding individual species.