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פותח על ידי קלירמאש פתרונות בע"מ -
Netmet: A network-based tool for predicting metabolic capacities of microbial species and their interactions
Year:
2020
Authors :
מדינה, שלומית
;
.
סלוואראג', גופינאת
;
.
עפאים, שני
;
.
פרייליך, שירי
;
.
Volume :
8
Co-Authors:

Tal, Ofir - Institute of Plant Sciences, Newe Ya’ar Research Center, The Agricultural Research Organization, Ramat Yishay, 30095, Israel.

Facilitators :
From page:
0
To page:
0
(
Total pages:
1
)
Abstract:

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. NetMet, a new web-based tool, is available at https://freilich-lab-tools.com/.

Note:
Related Files :
environment
Expansion algorithm
genomics
Metabolic networks
Microbial interactions
Network modeling
Simulation
עוד תגיות
תוכן קשור
More details
DOI :
10.3390/microorganisms8060840
Article number:
0
Affiliations:
Database:
סקופוס
Publication Type:
מאמר
;
.
Language:
אנגלית
Editors' remarks:
ID:
48276
Last updated date:
02/03/2022 17:27
Creation date:
15/06/2020 13:54
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Scientific Publication
Netmet: A network-based tool for predicting metabolic capacities of microbial species and their interactions
8

Tal, Ofir - Institute of Plant Sciences, Newe Ya’ar Research Center, The Agricultural Research Organization, Ramat Yishay, 30095, Israel.

Netmet: A network-based tool for predicting metabolic capacities of microbial species and their interactions

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. NetMet, a new web-based tool, is available at https://freilich-lab-tools.com/.

Scientific Publication
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