Network analysis methods for studying microbial communities: A mini review.
Microbial co-occurrence networks
Microbial interactions
Network analysis
Trans-kingdom interactions
Journal
Computational and structural biotechnology journal
ISSN: 2001-0370
Titre abrégé: Comput Struct Biotechnol J
Pays: Netherlands
ID NLM: 101585369
Informations de publication
Date de publication:
2021
2021
Historique:
received:
01
02
2021
revised:
01
05
2021
accepted:
01
05
2021
entrez:
7
6
2021
pubmed:
8
6
2021
medline:
8
6
2021
Statut:
epublish
Résumé
Microorganisms including bacteria, fungi, viruses, protists and archaea live as communities in complex and contiguous environments. They engage in numerous inter- and intra- kingdom interactions which can be inferred from microbiome profiling data. In particular, network-based approaches have proven helpful in deciphering complex microbial interaction patterns. Here we give an overview of state-of-the-art methods to infer intra-kingdom interactions ranging from simple correlation- to complex conditional dependence-based methods. We highlight common biases encountered in microbial profiles and discuss mitigation strategies employed by different tools and their trade-off with increased computational complexity. Finally, we discuss current limitations that motivate further method development to infer inter-kingdom interactions and to robustly and comprehensively characterize microbial environments in the future.
Identifiants
pubmed: 34093985
doi: 10.1016/j.csbj.2021.05.001
pii: S2001-0370(21)00182-3
pmc: PMC8131268
doi:
Types de publication
Journal Article
Review
Langues
eng
Pagination
2687-2698Informations de copyright
© 2021 The Authors. Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology.
Déclaration de conflit d'intérêts
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
Références
Bioinformatics. 2016 Mar 1;32(5):690-6
pubmed: 26520855
Front Microbiol. 2019 Mar 29;10:481
pubmed: 30984119
EBioMedicine. 2019 Aug;46:499-511
pubmed: 31327695
Theory Biosci. 2016 Jun;135(1-2):21-36
pubmed: 26762323
BMC Syst Biol. 2011;5 Suppl 2:S15
pubmed: 22784572
Brief Bioinform. 2021 Jul 20;22(4):
pubmed: 33264391
Bioinformatics. 2019 Jul 15;35(14):i23-i30
pubmed: 31510709
Cell Syst. 2017 Jan 25;4(1):129-137.e5
pubmed: 28125788
Microbiome. 2017 Nov 25;5(1):153
pubmed: 29178920
Genome Biol. 2014;15(7):R89
pubmed: 25146375
FEMS Microbiol Rev. 2018 Nov 1;42(6):761-780
pubmed: 30085090
PLoS Comput Biol. 2021 May 17;17(5):e1009021
pubmed: 33999922
FEMS Microbiol Rev. 2017 Jul 1;41(4):479-511
pubmed: 28430946
Mol Syst Biol. 2013 Apr 16;9:660
pubmed: 23591776
Bioinformatics. 2006 Jul 1;22(13):1623-30
pubmed: 16632496
Science. 2015 May 22;348(6237):1262073
pubmed: 25999517
Trends Microbiol. 2017 Mar;25(3):217-228
pubmed: 27916383
Nat Rev Microbiol. 2012 Jul 16;10(8):538-50
pubmed: 22796884
Nat Commun. 2017 Dec 11;8(1):2042
pubmed: 29229902
PLoS Comput Biol. 2012;8(9):e1002687
pubmed: 23028285
Front Microbiol. 2019 Feb 22;10:288
pubmed: 30846976
PLoS One. 2012;7(2):e30126
pubmed: 22319561
BMC Genomics. 2019 Apr 4;20(Suppl 2):187
pubmed: 30967118
BMC Bioinformatics. 2006 Mar 20;7 Suppl 1:S7
pubmed: 16723010
Bioinformatics. 2006 Oct 15;22(20):2532-8
pubmed: 16882654
Nat Med. 2019 Jun;25(6):1012-1021
pubmed: 31142849
Sci Rep. 2015 May 06;5:10007
pubmed: 25943705
Ann Appl Stat. 2019 Jun;13(2):848-873
pubmed: 31388390
PLoS Pathog. 2010 Jan 08;6(1):e1000713
pubmed: 20072605
F1000Res. 2016 Jun 27;5:1519
pubmed: 27853510
PLoS Comput Biol. 2020 May 29;16(5):e1007917
pubmed: 32469867
Microbiome. 2019 Aug 22;7(1):118
pubmed: 31439018
Bioinformatics. 2019 Sep 1;35(17):3055-3062
pubmed: 30657866
Nat Rev Microbiol. 2010 Oct;8(10):717-29
pubmed: 20805835
Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Feb;67(2 Pt 2):026126
pubmed: 12636767
Biostatistics. 2008 Jul;9(3):432-41
pubmed: 18079126
Front Genet. 2020 Jun 03;11:445
pubmed: 32582274
Front Genet. 2019 Jun 12;10:535
pubmed: 31249591
PLoS Comput Biol. 2012;8(7):e1002606
pubmed: 22807668
Front Microbiol. 2016 Sep 23;7:1508
pubmed: 27721810
Front Microbiol. 2017 Nov 15;8:2224
pubmed: 29187837
J Comput Biol. 2017 Jul;24(7):699-708
pubmed: 28489411
Microbiome. 2020 Jun 4;8(1):82
pubmed: 32498714
Mar Drugs. 2020 Jun 02;18(6):
pubmed: 32498449
Bioinform Biol Insights. 2015 Apr 29;9:61-74
pubmed: 25983554
Sci Rep. 2016 Feb 08;6:20359
pubmed: 26853461
NAR Genom Bioinform. 2020 Jun 25;2(2):lqaa042
pubmed: 33575595
PLoS Comput Biol. 2015 Mar 16;11(3):e1004075
pubmed: 25775355
Biometrics. 2019 Mar;75(1):235-244
pubmed: 30039859
iScience. 2019 Dec 20;22:380-391
pubmed: 31812808
Microbiome. 2018 Jan 15;6(1):12
pubmed: 29335027
Genome Biol. 2020 May 11;21(1):111
pubmed: 32393329
PLoS Comput Biol. 2015 May 07;11(5):e1004226
pubmed: 25950956
Biometrics. 2019 Jun;75(2):613-624
pubmed: 30387139
Bioinformatics. 2019 Sep 15;35(18):3404-3411
pubmed: 31220226
Proc Natl Acad Sci U S A. 2006 Aug 8;103(32):12115-20
pubmed: 16880384
Environ Pollut. 2017 Dec;231(Pt 1):908-917
pubmed: 28886536
Gut. 2018 Jun;67(6):1024-1032
pubmed: 28765474
Environ Microbiol. 2018 Feb;20(2):734-754
pubmed: 29235710
Microbiome. 2019 May 6;7(1):72
pubmed: 31060614
Sci Rep. 2018 Apr 12;8(1):5875
pubmed: 29651160
Trends Ecol Evol. 2005 Jun;20(6):345-53
pubmed: 16701391
Cell. 2018 Nov 1;175(4):973-983.e14
pubmed: 30388454
Cell. 2011 Mar 18;144(6):986-98
pubmed: 21414488
Gastrointest Tumors. 2015 May;2(1):26-32
pubmed: 26674881
Sci Rep. 2017 Nov 24;7(1):16252
pubmed: 29176663
Appl Environ Microbiol. 2008 Jan;74(1):172-81
pubmed: 17981942
Cell Syst. 2018 Apr 25;6(4):484-495.e5
pubmed: 29605183
BMC Bioinformatics. 2019 Jun 13;20(1):329
pubmed: 31195956
Genome Med. 2018 Feb 22;10(1):12
pubmed: 29471863
Cell. 2012 May 25;149(5):1164-73
pubmed: 22632978
Front Microbiol. 2018 Dec 19;9:3146
pubmed: 30619212
BMC Bioinformatics. 2012 May 30;13:113
pubmed: 22646978
J Clin Microbiol. 2010 Nov;48(11):4121-8
pubmed: 20826648
Cell Host Microbe. 2020 Nov 11;28(5):724-740.e8
pubmed: 32841606
BMC Bioinformatics. 2010 Feb 19;11:95
pubmed: 20170493
BMC Genomics. 2019 Apr 4;20(Suppl 2):185
pubmed: 30967122
Microbiome. 2019 Apr 2;7(1):54
pubmed: 30940197
J R Soc Interface. 2016 Mar;13(116):
pubmed: 26962029
Nat Rev Immunol. 2013 May;13(5):321-35
pubmed: 23618829
ISME J. 2012 Feb;6(2):343-51
pubmed: 21900968
J Comput Graph Stat. 2010 Sep 1;19(3):645-665
pubmed: 20877446
Nucleic Acids Res. 2016 Dec 15;44(22):e164
pubmed: 27596597
J Comput Biol. 2016 Jun;23(6):526-35
pubmed: 27267776
Bioinformatics. 2015 Oct 15;31(20):3322-9
pubmed: 26079350
Cell Syst. 2019 Sep 25;9(3):286-296.e8
pubmed: 31542415
Nat Commun. 2017 Sep 11;8(1):518
pubmed: 28894149
Sci Rep. 2017 Sep 18;7(1):11773
pubmed: 28924229
Adv Neural Inf Process Syst. 2010 Dec 31;24(2):1432-1440
pubmed: 25152607
Nature. 2011 May 12;473(7346):174-80
pubmed: 21508958
J Mach Learn Res. 2014 Oct;15:3297-3331
pubmed: 25620891
Microbiol Mol Biol Rev. 2019 Jan 9;83(1):
pubmed: 30626617
Ann Appl Stat. 2013 Mar 1;7(1):
pubmed: 24312162
PLoS One. 2019 Jul 24;14(7):e0207731
pubmed: 31339885
Nat Commun. 2014 Jul 08;5:4344
pubmed: 25003530
BMC Bioinformatics. 2020 Dec 28;21(Suppl 21):581
pubmed: 33371887
ISME J. 2013 Aug;7(8):1493-506
pubmed: 23575374
mSystems. 2021 Mar 16;6(2):
pubmed: 33727397
ISME J. 2016 Jul;10(7):1669-81
pubmed: 26905627
Gut. 2018 Aug;67(8):1454-1463
pubmed: 28988196
Bioinformatics. 2020 Mar 1;36(6):1840-1847
pubmed: 31697315
Microbiome. 2013 Jun 05;1(1):17
pubmed: 24450808
Bioinformatics. 2015 Oct 1;31(19):3172-80
pubmed: 26048598
Curr Opin Microbiol. 2015 Jun;25:56-66
pubmed: 26005845
Mol Syst Biol. 2018 Jun 20;14(6):e8124
pubmed: 29925568
Microbiome. 2016 Apr 12;4:15
pubmed: 27068581
Proc Natl Acad Sci U S A. 2014 Jan 7;111(1):439-44
pubmed: 24367073
BMC Bioinformatics. 2007 Aug 14;8:299
pubmed: 17697349