{"doi":"10.3390/microorganisms8060840","title":"NetMet: A Network-Based Tool for Predicting Metabolic Capacities of Microbial Species and their Interactions","abstract":"<jats:p>Metabolic conversions allow organisms to produce a set of essential metabolites from the available nutrients in an environment, frequently requiring metabolic exchanges among co-inhabiting organisms. Genomic-based metabolic simulations are being increasingly applied for exploring metabolic capacities, considering different environments and different combinations of microorganisms. NetMet is a web-based tool and a software package for predicting the metabolic performances of microorganisms and their corresponding combinations in user-defined environments. The algorithm takes, as input, lists of (i) species-specific enzymatic reactions (EC numbers), and (ii) relevant metabolic environments. The algorithm generates, as output, lists of (i) compounds that individual species can produce in each given environment, and (ii) compounds that are predicted to be produced through complementary interactions. The tool is demonstrated in two case studies. First, we compared the metabolic capacities of different haplotypes of the obligatory fruit and vegetable pathogen Candidatus Liberibacter solanacearum to those of their culturable taxonomic relative Liberibacter crescens. Second, we demonstrated the potential production of complementary metabolites by pairwise combinations of co-occurring endosymbionts of the plant phloem-feeding whitefly Bemisia tabaci.</jats:p>","journal":"Microorganisms","year":2020,"id":618177,"datarank":0.4636563680037475,"base_score":3.091042453358316,"endowment":3.091042453358316,"self_citation_contribution":0.4636563680037475,"citation_network_contribution":0.0,"self_endowment_contribution":0.4636563680037475,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":21,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1594560,"name":"Gopinath Selvaraj","orcid":null,"position":1,"is_corresponding":false},{"id":1594561,"name":"Shlomit Medina","orcid":null,"position":2,"is_corresponding":false},{"id":1016672,"name":"Shany Ofaim","orcid":"0000-0001-8641-7007","position":3,"is_corresponding":false},{"id":1594562,"name":"Shiri Freilich","orcid":"0000-0002-5173-9695","position":4,"is_corresponding":false},{"id":1594559,"name":"Ofir Tal","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"NetMet: A Network-Based Tool for Predicting Metabolic Capacities of Microbial Species and their Interactions","abstract":"<jats:p>Metabolic conversions allow organisms to produce a set of essential metabolites from the available nutrients in an environment, frequently requiring metabolic exchanges among co-inhabiting organisms. Genomic-based metabolic simulations are being increasingly applied for exploring metabolic capacities, considering different environments and different combinations of microorganisms. NetMet is a web-based tool and a software package for predicting the metabolic performances of microorganisms and their corresponding combinations in user-defined environments. The algorithm takes, as input, lists of (i) species-specific enzymatic reactions (EC numbers), and (ii) relevant metabolic environments. The algorithm generates, as output, lists of (i) compounds that individual species can produce in each given environment, and (ii) compounds that are predicted to be produced through complementary interactions. The tool is demonstrated in two case studies. First, we compared the metabolic capacities of different haplotypes of the obligatory fruit and vegetable pathogen Candidatus Liberibacter solanacearum to those of their culturable taxonomic relative Liberibacter crescens. Second, we demonstrated the potential production of complementary metabolites by pairwise combinations of co-occurring endosymbionts of the plant phloem-feeding whitefly Bemisia tabaci.</jats:p>","is_dataset_classified":null,"base_score":3.091042453358316,"endowment":3.091042453358316,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"32503277","pmcid":"PMC7356744","openalex_id":"https://openalex.org/W3033983517","authors":[],"funders":[{"funder_name":"Israel Science Foundation","grant_id":"484/17","title":null},{"funder_name":"Centre National pour la Recherche Scientifique et Technique","grant_id":"N/A","title":null}],"total_grants":2,"fwci":2.4543,"citation_percentile":0.87997769,"influential_citations":0,"citation_trend":[{"year":2021,"count":7},{"year":2022,"count":4},{"year":2023,"count":3},{"year":2024,"count":5},{"year":2025,"count":1},{"year":2026,"count":1}],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://www.mdpi.com/2076-2607/8/6/840/pdf?version=1592481583","host_type":"journal"},{"url":"https://www.mdpi.com/2076-2607/8/6/840/pdf?version=1592481583","host_type":"publisher"},{"url":"https://www.mdpi.com/2076-2607/8/6/840/pdf","host_type":"publisher"},{"url":"https://doi.org/10.3390/microorganisms8060840","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/32503277","host_type":"repository"},{"url":"https://doaj.org/article/9344a50900264131b1e5096520d68b3f","host_type":"repository"},{"url":"http://dx.doi.org/10.3390/microorganisms8060840","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7356744","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC7356744","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC7356744?pdf=render","host_type":"Europe_PMC"}],"fields_of_study":["Insect symbiosis and bacterial influences","Phytoplasmas and Hemiptera pathogens","Insect-Plant Interactions and Control"],"mesh_terms":[],"keywords":["Metabolic network","Pairwise comparison","Biology","Metabolic pathway","Metabolic activity","Metabolic engineering","Microorganism","Computational biology","Bacteria","Computer science","Biochemistry","Metabolism","Biological system","Enzyme","Genetics","Artificial intelligence","Simulation","Environment","Genomics","Network Modeling","Metabolic Networks","Microbial Interactions","Expansion Algorithm"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Life in Land"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-03T03:40:28.875665Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}