NetCom: A Network-Based Tool for Predicting Metabolic Activities of Microbial Communities Based on Interpretation of Metagenomics Data.
metabolic networks
metagenomics
microbial communities
Journal
Microorganisms
ISSN: 2076-2607
Titre abrégé: Microorganisms
Pays: Switzerland
ID NLM: 101625893
Informations de publication
Date de publication:
30 Aug 2021
30 Aug 2021
Historique:
received:
06
06
2021
revised:
08
08
2021
accepted:
18
08
2021
entrez:
28
9
2021
pubmed:
29
9
2021
medline:
29
9
2021
Statut:
epublish
Résumé
The study of microbial activity can be viewed as a triangle with three sides: environment (dominant resources in a specific habitat), community (species dictating a repertoire of metabolic conversions) and function (production and/or utilization of resources and compounds). Advances in metagenomics enable a high-resolution description of complex microbial communities in their natural environments and support a systematic study of environment-community-function associations. NetCom is a web-tool for predicting metabolic activities of microbial communities based on network-based interpretation of assembled and annotated metagenomics data. The algorithm takes as an input, lists of differentially abundant enzymatic reactions and generates the following outputs: (i) pathway associations of differently abundant enzymes; (ii) prediction of environmental resources that are unique to each treatment, and their pathway associations; (iii) prediction of compounds that are produced by the microbial community, and pathway association of compounds that are treatment-specific; (iv) network visualization of enzymes, environmental resources and produced compounds, that are treatment specific (2 and 3D). The tool is demonstrated on metagenomic data from rhizosphere and bulk soil samples. By predicting root-specific activities, we illustrate the relevance of our framework for forecasting the impact of soil amendments on the corresponding microbial communities. NetCom is available online.
Identifiants
pubmed: 34576734
pii: microorganisms9091838
doi: 10.3390/microorganisms9091838
pmc: PMC8468097
pii:
doi:
Types de publication
Journal Article
Langues
eng
Subventions
Organisme : United States - Israel Binational Agricultural Research and Development Fund
ID : US-5046-17R
Organisme : Israel Science Foundation
ID : NSFC-ISF joint program (4181101565), Israel Science Foundation Grant no. 3164/19
Références
mSystems. 2019 May 28;4(3):
pubmed: 31138719
mSystems. 2016 Jan-Feb;1(1):
pubmed: 27239563
Proc Natl Acad Sci U S A. 2015 May 19;112(20):6449-54
pubmed: 25941371
Nucleic Acids Res. 2019 Jan 8;47(D1):D590-D595
pubmed: 30321428
Plant Signal Behav. 2009 Aug;4(8):777-80
pubmed: 19820328
Curr Opin Microbiol. 2015 Oct;27:37-44
pubmed: 26207681
Appl Environ Microbiol. 2015 Oct 16;82(1):157-66
pubmed: 26475107
Proc Natl Acad Sci U S A. 2008 Sep 23;105(38):14482-7
pubmed: 18787117
PLoS Comput Biol. 2016 Apr 15;12(4):e1004875
pubmed: 27081850
BioData Min. 2011 Apr 28;4:10
pubmed: 21527005
Proc Natl Acad Sci U S A. 2006 Dec 5;103(49):18389-94
pubmed: 17130454
FEMS Microbiol Lett. 2007 Mar;268(1):34-9
pubmed: 17227464
Nat Biotechnol. 2017 Jan;35(1):81-89
pubmed: 27893703
Environ Int. 2011 Nov;37(8):1362-75
pubmed: 21722961
Nat Rev Microbiol. 2012 Apr 11;10(5):323-35
pubmed: 22491358
Curr Opin Biotechnol. 2013 Jun;24(3):474-81
pubmed: 22999827
BMC Genomics. 2018 May 25;19(1):402
pubmed: 29801436
PLoS One. 2015 Aug 18;10(8):e0135868
pubmed: 26285202
Nat Plants. 2018 May;4(5):247-257
pubmed: 29725101
PLoS Comput Biol. 2010 Feb 26;6(2):e1000690
pubmed: 20195496
Appl Environ Microbiol. 2002 Jul;68(7):3328-38
pubmed: 12089011
Front Microbiol. 2015 Mar 19;6:213
pubmed: 25852671
Antonie Van Leeuwenhoek. 2002 Aug;81(1-4):257-61
pubmed: 12448724
Curr Opin Biotechnol. 2021 Feb;67:184-191
pubmed: 33592536
Nat Commun. 2011 Dec 13;2:589
pubmed: 22158444
Genome Inform. 2004;15(1):35-45
pubmed: 15712108
Nat Commun. 2014 Sep 18;5:4950
pubmed: 25232638
Curr Opin Biotechnol. 2013 Aug;24(4):810-20
pubmed: 23623295
NPJ Biofilms Microbiomes. 2015 Jun 17;1:15007
pubmed: 28721231
Proc Natl Acad Sci U S A. 1999 Apr 27;96(9):4786-90
pubmed: 10220371
Front Microbiol. 2014 Mar 26;5:125
pubmed: 24723922
Phytopathology. 1997 Jul;87(7):720-9
pubmed: 18945094
Bioinformatics. 2010 Jan 1;26(1):139-40
pubmed: 19910308
Front Microbiol. 2017 Aug 23;8:1606
pubmed: 28878756
Front Microbiol. 2016 May 18;7:673
pubmed: 27242701
Annu Rev Phytopathol. 2004;42:35-59
pubmed: 15283659
Brief Bioinform. 2012 Nov;13(6):769-80
pubmed: 22589385
Bioinformatics. 2012 Mar 1;28(5):734-5
pubmed: 22219204
Open Microbiol J. 2015 Mar 31;9:1-7
pubmed: 25926899
Phytopathology. 2017 Mar;107(3):256-263
pubmed: 27898265
Microorganisms. 2020 Jun 03;8(6):
pubmed: 32503277
Protein Sci. 2019 Nov;28(11):1947-1951
pubmed: 31441146
Science. 2009 May 29;324(5931):1150-1
pubmed: 19478170
Nature. 2009 May 14;459(7244):193-9
pubmed: 19444205
Nucleic Acids Res. 2008 Jan;36(Database issue):D480-4
pubmed: 18077471
ACS Synth Biol. 2014 Apr 18;3(4):247-57
pubmed: 24742179
PLoS Comput Biol. 2012;8(12):e1002832
pubmed: 23284280
Bioinformatics. 2012 Aug 15;28(16):2195-7
pubmed: 22668793
J Mol Biol. 2016 Feb 27;428(5 Pt B):837-61
pubmed: 26522937
Nucleic Acids Res. 2000 Jan 1;28(1):27-30
pubmed: 10592173
Curr Opin Microbiol. 2014 Apr;18:72-7
pubmed: 24632350
Mol Syst Biol. 2013 May 14;9:666
pubmed: 23670539
Mol Syst Biol. 2007;3:92
pubmed: 17353934
ISME J. 2016 Nov;10(11):2557-2568
pubmed: 27022995
Environ Microbiol. 2014 Jul;16(7):2157-67
pubmed: 23962203