Unlocking the microbial studies through computational approaches: how far have we reached?
Artificial intelligence
Deep learning
Machine learning
Metagenomics
Microbiology
Journal
Environmental science and pollution research international
ISSN: 1614-7499
Titre abrégé: Environ Sci Pollut Res Int
Pays: Germany
ID NLM: 9441769
Informations de publication
Date de publication:
Apr 2023
Apr 2023
Historique:
received:
23
03
2022
accepted:
24
02
2023
medline:
18
4
2023
pubmed:
16
3
2023
entrez:
15
3
2023
Statut:
ppublish
Résumé
The metagenomics approach accelerated the study of genetic information from uncultured microbes and complex microbial communities. In silico research also facilitated an understanding of protein-DNA interactions, protein-protein interactions, docking between proteins and phyto/biochemicals for drug design, and modeling of the 3D structure of proteins. These in silico approaches provided insight into analyzing pathogenic and nonpathogenic strains that helped in the identification of probable genes for vaccines and antimicrobial agents and comparing whole-genome sequences to microbial evolution. Artificial intelligence, more precisely machine learning (ML) and deep learning (DL), has proven to be a promising approach in the field of microbiology to handle, analyze, and utilize large data that are generated through nucleic acid sequencing and proteomics. This enabled the understanding of the functional and taxonomic diversity of microorganisms. ML and DL have been used in the prediction and forecasting of diseases and applied to trace environmental contaminants and environmental quality. This review presents an in-depth analysis of the recent application of silico approaches in microbial genomics, proteomics, functional diversity, vaccine development, and drug design.
Identifiants
pubmed: 36920617
doi: 10.1007/s11356-023-26220-0
pii: 10.1007/s11356-023-26220-0
pmc: PMC10016191
doi:
Substances chimiques
DNA
9007-49-2
Types de publication
Journal Article
Review
Langues
eng
Sous-ensembles de citation
IM
Pagination
48929-48947Informations de copyright
© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.
Références
Bioinformatics. 2019 Jul 1;35(13):2276-2282
pubmed: 30462147
Nucleic Acids Res. 2016 Aug 19;44(14):6614-24
pubmed: 27342282
Genome Biol. 2022 Jun 20;23(1):133
pubmed: 35725628
Diagnostics (Basel). 2020 Nov 26;10(12):
pubmed: 33256024
Interdiscip Sci. 2017 Dec;9(4):540-544
pubmed: 27739055
Comb Chem High Throughput Screen. 2019;22(10):683-693
pubmed: 31782356
Mini Rev Med Chem. 2018;18(3):196-207
pubmed: 28302041
Nucleic Acids Res. 2017 Oct 13;45(18):e159
pubmed: 29048594
BMC Med Genomics. 2017 Dec 28;10(Suppl 5):76
pubmed: 29297351
Nat Commun. 2022 Mar 10;13(1):1265
pubmed: 35273146
PLoS One. 2013 Jul 29;8(7):e69885
pubmed: 23922841
Curr Opin Biotechnol. 2013 Jun;24(3):526-33
pubmed: 23183250
Trends Biotechnol. 2011 Sep;29(9):464-72
pubmed: 21680034
BMC Genom Data. 2022 Jun 6;23(1):43
pubmed: 35668373
Bioinformatics. 2018 May 15;34(10):1666-1671
pubmed: 29240876
Eur J Med Chem. 2020 Dec 1;207:112764
pubmed: 32871340
Curr Opin Microbiol. 2004 Oct;7(5):492-8
pubmed: 15451504
Nat Rev Drug Discov. 2019 Jun;18(6):463-477
pubmed: 30976107
FEMS Microbiol Lett. 2004 Feb 16;231(2):153-8
pubmed: 15027428
PeerJ. 2015 May 28;3:e985
pubmed: 26038737
PLoS Comput Biol. 2022 Sep 30;18(9):e1010493
pubmed: 36178955
Microbiome. 2018 Feb 01;6(1):23
pubmed: 29391044
Int J Mol Sci. 2018 Feb 08;19(2):
pubmed: 29419752
Mini Rev Med Chem. 2014 Apr;14(4):345-54
pubmed: 24552264
Biomed Res Int. 2016;2016:1654623
pubmed: 27437396
J Pers Med. 2020 Feb 27;10(1):
pubmed: 32120849
Proc Natl Acad Sci U S A. 2009 Jul 7;106(27):11352-7
pubmed: 19541615
Nat Genet. 2013 Oct;45(10):1255-60
pubmed: 23995137
Bioinformatics. 2015 Nov 15;31(22):3691-3
pubmed: 26198102
Mol Biosyst. 2014 Dec;10(12):3147-54
pubmed: 25230581
Bioinformatics. 2018 Jan 15;34(2):292-293
pubmed: 29028899
PeerJ. 2020 Oct 27;8:e10121
pubmed: 33194387
Pak J Pharm Sci. 2021 Mar;34(2):553-560
pubmed: 34275829
J Biomol Struct Dyn. 2021 Oct;39(16):6195-6217
pubmed: 32686993
Bioinformatics. 2017 Nov 01;33(21):3473-3476
pubmed: 29077805
Cell. 2011 Sep 30;147(1):44-56
pubmed: 21962506
Bioinformatics. 2013 Oct 15;29(20):2617-24
pubmed: 24002109
PLoS Comput Biol. 2020 Mar 5;16(3):e1007134
pubmed: 32134915
BMC Med Genomics. 2015;8 Suppl 2:S2
pubmed: 26044949
Nucleic Acids Res. 2017 Jan 4;45(D1):D491-D498
pubmed: 27789703
Microbiol Mol Biol Rev. 2004 Dec;68(4):669-85
pubmed: 15590779
Genome Biol. 2002;3(2):REVIEWS0003
pubmed: 11864374
Nat Rev Microbiol. 2005 Jun;3(6):504-10
pubmed: 15886693
BMC Genomics. 2017 Jul 10;18(1):521
pubmed: 28693474
Annu Rev Genet. 2004;38:525-52
pubmed: 15568985
Nucleic Acids Res. 2017 Jan 4;45(D1):D574-D580
pubmed: 27899569
Comput Struct Biotechnol J. 2021 Jan 27;19:1092-1107
pubmed: 33680353
J Am Soc Mass Spectrom. 2021 Jun 2;32(6):1295-1299
pubmed: 33856212
Brief Funct Genomics. 2016 Jan;15(1):55-64
pubmed: 26134276
Antimicrob Agents Chemother. 2020 Mar 24;64(4):
pubmed: 31932376
Genome Biol. 2016 Nov 25;17(1):238
pubmed: 27887642
Nucleic Acids Res. 2015 Jul 1;43(W1):W65-71
pubmed: 25958395
Int J Proteomics. 2014;2014:147648
pubmed: 24693427
Environ Sci Pollut Res Int. 2021 Oct;28(38):52798-52809
pubmed: 34476696
Bioinformatics. 2010 Oct 1;26(19):2460-1
pubmed: 20709691
Microbiol Resour Announc. 2021 Mar 4;10(9):
pubmed: 33664143
Emerg Infect Dis. 2017 Dec;23(13):
pubmed: 29155671
Mol Ther Nucleic Acids. 2018 Dec 7;13:464-471
pubmed: 30388620
Mol Biosyst. 2017 Aug 22;13(9):1781-1787
pubmed: 28702594
Expert Rev Mol Diagn. 2017 Mar;17(3):225-237
pubmed: 28092471
Brief Bioinform. 2018 Sep 28;19(5):1022-1034
pubmed: 28398567
Bioinformatics. 2019 Nov 1;35(21):4453-4455
pubmed: 31070718
BMC Bioinformatics. 2019 Dec 12;20(1):665
pubmed: 31830921
J Bioinform Comput Biol. 2017 Feb;15(1):1650024
pubmed: 27397631
Viruses. 2020 May 19;12(5):
pubmed: 32438586
Nucleic Acids Res. 2021 Jul 2;49(W1):W293-W296
pubmed: 33885785
Genome Biol. 2014;15(11):524
pubmed: 25410596
Lancet Infect Dis. 2015 Oct;15(10):1193-1202
pubmed: 26116186
BMC Bioinformatics. 2012 May 08;13:87
pubmed: 22568821
J Pers Med. 2020 Mar 01;10(1):
pubmed: 32121555
RNA Biol. 2018;15(6):797-806
pubmed: 29583068
J Comput Biol. 2019 Jun;26(6):519-535
pubmed: 31050550
BMC Genomics. 2008 Feb 08;9:75
pubmed: 18261238
BMC Bioinformatics. 2018 Jun 15;19(1):227
pubmed: 29907097
Annu Rev Microbiol. 1986;40:337-65
pubmed: 2430518
Brief Bioinform. 2020 Jan 17;21(1):298-308
pubmed: 30403770
Protein Cell. 2021 May;12(5):315-330
pubmed: 32394199
J Mol Microbiol Biotechnol. 2009;16(1-2):25-37
pubmed: 18957860
IEEE/ACM Trans Comput Biol Bioinform. 2019 Jul-Aug;16(4):1231-1239
pubmed: 30040651
Front Microbiol. 2019 Apr 16;10:620
pubmed: 31040829
Microbiome. 2017 Jul 6;5(1):69
pubmed: 28683828
Antimicrob Agents Chemother. 2016 May 23;60(6):3821-3
pubmed: 27001821
Comb Chem High Throughput Screen. 2019;22(10):665-674
pubmed: 31782358
Cell. 2020 Apr 16;181(2):475-483
pubmed: 32302574
Gigascience. 2020 Oct 15;9(10):
pubmed: 33057676
Cells. 2020 May 21;9(5):
pubmed: 32455748
Inf Fusion. 2019 Oct;50:71-91
pubmed: 30467459
BMC Syst Biol. 2016 Dec 23;10(Suppl 4):111
pubmed: 28155709
ACS Chem Biol. 2019 Apr 19;14(4):758-766
pubmed: 30830745
Curr Opin Microbiol. 2002 Oct;5(5):520-4
pubmed: 12354561
Nature. 2020 Mar;579(7800):567-574
pubmed: 32214244
Database (Oxford). 2009;2009:bap021
pubmed: 20157493
Bioinformatics. 2021 Jul 19;37(12):1673-1680
pubmed: 33471068
mSystems. 2020 Aug 4;5(4):
pubmed: 32753501
Bioinformatics. 2015 Mar 1;31(5):761-3
pubmed: 25338716
PLoS Comput Biol. 2017 Dec 18;13(12):e1005912
pubmed: 29253885
Bioinformatics. 2017 Mar 1;33(5):733-739
pubmed: 28025197
Trends Genet. 2010 Oct;26(10):449-57
pubmed: 20739089
BMC Bioinformatics. 2013 Nov 02;14:315
pubmed: 24180526
BMC Bioinformatics. 2017 Apr 11;18(1):208
pubmed: 28399797
BMC Bioinformatics. 2020 Oct 31;21(1):492
pubmed: 33129268
Chem Sci. 2021 Jun 7;12(26):9221-9232
pubmed: 34349895
Front Genet. 2018 Aug 07;9:304
pubmed: 30131825
J Membr Biol. 2011 Jan;239(1-2):27-34
pubmed: 21225255
PLoS One. 2010 Mar 10;5(3):e9490
pubmed: 20224823
Microbiome. 2017 Oct 12;5(1):134
pubmed: 29020980
Am J Trop Med Hyg. 2005 Aug;73(2):256-62
pubmed: 16103584
BMC Bioinformatics. 2019 Dec 23;20(1):730
pubmed: 31870282
PLoS Comput Biol. 2015 Feb 12;11(2):e1004041
pubmed: 25675341
BMC Bioinformatics. 2016 Aug 31;17 Suppl 8:282
pubmed: 27585458
Bioinformatics. 2019 Feb 15;35(4):593-601
pubmed: 30052767
BMC Bioinformatics. 2010 Mar 08;11:119
pubmed: 20211023
Environ Sci Pollut Res Int. 2021 Aug;28(30):40431-40444
pubmed: 33447984
Front Bioinform. 2021 Jun 17;1:669186
pubmed: 36303723
Antimicrob Agents Chemother. 2015 Oct;59(10):6096-100
pubmed: 26195521
Bioinformatics. 2018 Aug 15;34(16):2740-2747
pubmed: 29590297
Artif Intell Med. 2017 Mar;77:53-63
pubmed: 28545612
Curr Pharm Biotechnol. 2019;20(14):1163-1171
pubmed: 31433750
Bioinformatics. 2017 Jan 1;33(1):128-129
pubmed: 27605102
J Mol Biol. 2020 Feb 14;432(4):845-860
pubmed: 31874151
IEEE/ACM Trans Comput Biol Bioinform. 2019 Jan-Feb;16(1):283-291
pubmed: 29990255
Microb Genom. 2016 Nov 30;2(11):e000093
pubmed: 28348833
Biochim Biophys Acta. 2014 Oct;1842(10):1932-1941
pubmed: 24995601
Environ Microbiol. 2004 Sep;6(9):981-9
pubmed: 15305923
Curr Pharm Des. 2016;22(5):572-81
pubmed: 26601966
Front Pharmacol. 2021 May 12;12:652335
pubmed: 34054532
Bioinformatics. 2014 Jul 15;30(14):2068-9
pubmed: 24642063
mSystems. 2022 Oct 26;7(5):e0074122
pubmed: 36069454
Genome Res. 2014 Jul;24(7):1180-92
pubmed: 24899342
FEMS Microbiol Rev. 2021 Sep 8;45(5):
pubmed: 33724378
Anal Biochem. 1996 Nov 1;242(1):84-9
pubmed: 8923969
BMC Bioinformatics. 2019 Jan 23;20(1):48
pubmed: 30674273
Virology. 2017 Mar;503:21-30
pubmed: 28110145
Annu Rev Microbiol. 2003;57:369-94
pubmed: 14527284
Nucleic Acids Res. 2015 Feb 18;43(3):e15
pubmed: 25414349