Directed Evolution of Microbial Communities.
artificial ecosystem selection
collective community functions
directed evolution
microbial communities
structure–function landscape
Journal
Annual review of biophysics
ISSN: 1936-1238
Titre abrégé: Annu Rev Biophys
Pays: United States
ID NLM: 101469708
Informations de publication
Date de publication:
06 05 2021
06 05 2021
Historique:
pubmed:
2
3
2021
medline:
28
5
2021
entrez:
1
3
2021
Statut:
ppublish
Résumé
Directed evolution is a form of artificial selection that has been used for decades to find biomolecules and organisms with new or enhanced functional traits. Directed evolution can be conceptualized as a guided exploration of the genotype-phenotype map, where genetic variants with desirable phenotypes are first selected and then mutagenized to search the genotype space for an even better mutant. In recent years, the idea of applying artificial selection to microbial communities has gained momentum. In this article, we review the main limitations of artificial selection when applied to large and diverse collectives of asexually dividing microbes and discuss how the tools of directed evolution may be deployed to engineer communities from the top down. We conceptualize directed evolution of microbial communities as a guided exploration of an ecological structure-function landscape and propose practical guidelines for navigating these ecological landscapes.
Identifiants
pubmed: 33646814
doi: 10.1146/annurev-biophys-101220-072829
pmc: PMC8105285
mid: NIHMS1681821
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Review
Langues
eng
Sous-ensembles de citation
IM
Pagination
323-341Subventions
Organisme : NIGMS NIH HHS
ID : R35 GM133467
Pays : United States
Références
Nature. 2013 Aug 8;500(7461):203-6
pubmed: 23851393
J R Soc Interface. 2017 Feb;14(127):
pubmed: 28148770
Ecol Lett. 2015 Oct;18(10):1040-8
pubmed: 26259498
Proc Natl Acad Sci U S A. 2007 May 15;104 Suppl 1:8641-8
pubmed: 17494757
Nature. 2009 May 14;459(7244):253-6
pubmed: 19349960
mSystems. 2021 Dec 21;6(6):e0112521
pubmed: 34846165
Nature. 2011 Apr 28;472(7344):499-503
pubmed: 21478873
Evol Appl. 2020 Jul 28;13(9):2460-2471
pubmed: 33005234
Appl Environ Microbiol. 2005 Nov;71(11):7099-106
pubmed: 16269746
Curr Treat Options Gastroenterol. 2015 Mar;13(1):105-20
pubmed: 25595930
Proc Natl Acad Sci U S A. 2012 Jan 31;109(5):1595-600
pubmed: 22307617
Evolution. 1977 Mar;31(1):134-153
pubmed: 28567731
Trends Ecol Evol. 2015 Aug;30(8):470-6
pubmed: 26111582
Nature. 2008 Aug 21;454(7207):987-90
pubmed: 18719588
PLoS Comput Biol. 2016 Feb 01;12(2):e1004685
pubmed: 26829588
Curr Opin Struct Biol. 2005 Aug;15(4):472-8
pubmed: 16043338
Curr Biol. 2017 Nov 6;27(21):3390-3395.e4
pubmed: 29107553
Nature. 2018 May;557(7705):434-438
pubmed: 29743671
Proc Natl Acad Sci U S A. 2004 Jan 13;101(2):580-5
pubmed: 14704282
Science. 1992 Jul 31;257(5070):635-41
pubmed: 1496376
Evolution. 1990 Sep;44(6):1625-1636
pubmed: 28564304
Proc Natl Acad Sci U S A. 2009 Jun 16;106 Suppl 1:9971-8
pubmed: 19528637
Tetrahedron. 2016 Jun 23;72(25):3609-3624
pubmed: 27429480
Cell. 2014 Jul 17;158(2):422-433
pubmed: 25036636
Ecol Lett. 2010 Jun;13(6):675-84
pubmed: 20412280
Nat Rev Mol Cell Biol. 2009 Dec;10(12):866-76
pubmed: 19935669
Elife. 2018 Apr 17;7:
pubmed: 29664397
Evol Med Public Health. 2018 Mar 08;2018(1):60-66
pubmed: 29588855
PLoS Biol. 2013;11(4):e1001547
pubmed: 23637571
Antibiotics (Basel). 2018 Feb 13;7(1):
pubmed: 29438355
Cell Host Microbe. 2017 Aug 9;22(2):142-155
pubmed: 28799900
Science. 2001 Oct 26;294(5543):843-5
pubmed: 11679667
Evolution. 1990 Sep;44(6):1614-1624
pubmed: 28564309
Curr Biol. 2015 Apr 20;25(8):1043-9
pubmed: 25772450
Microb Biotechnol. 2020 Nov;13(6):1748-1764
pubmed: 32639625
ISME J. 2020 Oct;14(10):2505-2513
pubmed: 32555503
PLoS Biol. 2019 Aug 30;17(8):e3000356
pubmed: 31469824
PLoS Biol. 2018 Feb 20;16(2):e2003962
pubmed: 29462153
PLoS Biol. 2019 Dec 12;17(12):e3000550
pubmed: 31830028
Sci Adv. 2020 Feb 19;6(8):eaay8676
pubmed: 32128414
Methods Mol Biol. 2014;1179:103-28
pubmed: 25055773
Curr Opin Chem Biol. 2009 Feb;13(1):3-9
pubmed: 19249235
Nature. 1994 Aug 4;370(6488):389-91
pubmed: 8047147
Proc Natl Acad Sci U S A. 2004 Jul 6;101(27):10101-6
pubmed: 15220472
Philos Trans R Soc Lond B Biol Sci. 2020 May 11;375(1798):20190681
pubmed: 32200751
Antimicrob Agents Chemother. 2016 Jun 20;60(7):4264-73
pubmed: 27161626
Chem Rev. 1997 Apr 1;97(2):391-410
pubmed: 11848876
Cell. 2009 Dec 24;139(7):1366-75
pubmed: 20064380
Science. 2001 Oct 26;294(5543):804-8
pubmed: 11679658
Trends Microbiol. 2015 Oct;23(10):606-617
pubmed: 26422463
Nat Ecol Evol. 2017 Mar 27;1(5):109
pubmed: 28812687
Nat Commun. 2013;4:2742
pubmed: 24193369
Nat Rev Genet. 2015 Jul;16(7):379-94
pubmed: 26055155
Proc Natl Acad Sci U S A. 2000 Aug 1;97(16):9110-4
pubmed: 10890915
Proc Natl Acad Sci U S A. 2007 May 22;104(21):8918-23
pubmed: 17517642
PLoS Comput Biol. 2021 Jan 22;17(1):e1008643
pubmed: 33481772
Science. 2009 Jan 9;323(5911):272-5
pubmed: 19131632
PLoS One. 2019 Dec 4;14(12):e0225933
pubmed: 31800619
Front Bioeng Biotechnol. 2020 Jul 22;8:834
pubmed: 32793576
Microb Ecol. 2018 Aug;76(2):419-429
pubmed: 29392382
Philos Trans R Soc Lond B Biol Sci. 2011 May 12;366(1569):1401-9
pubmed: 21444314
Annu Rev Genet. 1982;16:1-19
pubmed: 6760797
J Biotechnol. 2012 Jan;157(1):189-97
pubmed: 22079750
PLoS Biol. 2019 Jun 25;17(6):e3000295
pubmed: 31237866
ISME J. 2015 Mar 17;9(4):980-9
pubmed: 25350154
Trends Genet. 2016 Apr;32(4):189-200
pubmed: 26916078
Nat Methods. 2019 Feb;16(2):167-170
pubmed: 30643213
Appl Microbiol Biotechnol. 2016 Sep;100(17):7713-25
pubmed: 27170322
Proc Natl Acad Sci U S A. 1992 Aug 15;89(16):7811-5
pubmed: 1502200
ACS Synth Biol. 2019 Sep 20;8(9):2174-2185
pubmed: 31461261
Viruses. 2019 Mar 11;11(3):
pubmed: 30862096
Mol Syst Biol. 2010 Apr 13;6:357
pubmed: 20393577
Proc Biol Sci. 2006 Oct 7;273(1600):2565-70
pubmed: 16959650
Proc Natl Acad Sci U S A. 2000 Aug 15;97(17):9365-6
pubmed: 10944208
Front Microbiol. 2016 Dec 06;7:1967
pubmed: 27999571
Elife. 2020 Jul 07;9:
pubmed: 32633717
Microb Cell Fact. 2010 Feb 16;9:10
pubmed: 20158909
Microbiome. 2019 Jun 3;7(1):85
pubmed: 31159875
Microb Ecol. 2006 Aug;52(2):280-8
pubmed: 16897310
Nature. 2011 Jan 13;469(7329):207-11
pubmed: 21150900
Evolution. 2020 Oct;74(10):2392-2403
pubmed: 32888315
Science. 2012 Jun 1;336(6085):1175-7
pubmed: 22654061
Appl Environ Microbiol. 1999 Aug;65(8):3697-704
pubmed: 10427068
Curr Opin Biotechnol. 2019 Aug;58:117-128
pubmed: 30952088
PeerJ. 2020 Jul 1;8:e9350
pubmed: 32676220
Microb Ecol. 2017 Feb;73(2):394-403
pubmed: 27655524
Elife. 2015 Aug 24;4:
pubmed: 26302311
Sci Transl Med. 2014 Jan 22;6(220):220ra11
pubmed: 24452263
Front Microbiol. 2020 Jan 10;10:3010
pubmed: 31998278
Elife. 2016 Jun 16;5:
pubmed: 27310530
Environ Microbiol. 2000 Oct;2(5):564-71
pubmed: 11233164
Proc Natl Acad Sci U S A. 2009 Jun 16;106 Suppl 1:9995-10000
pubmed: 19528653
Bioresour Technol. 2013 May;136:697-706
pubmed: 23566469
Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16587-91
pubmed: 12451174
Genetics. 1978 Jul;89(3):453-65
pubmed: 97169
Nat Commun. 2014 May 02;5:3713
pubmed: 24785661
PLoS Comput Biol. 2016 Sep 13;12(9):e1005079
pubmed: 27623159
Bioscience. 2011 May;61(5):398-406
pubmed: 21731083
Proc Natl Acad Sci U S A. 2014 Dec 16;111(50):17803-8
pubmed: 25453111
Proc Natl Acad Sci U S A. 1976 Dec;73(12):4604-7
pubmed: 1070012
Proc Natl Acad Sci U S A. 2022 Feb 8;119(6):
pubmed: 35105804
Nature. 2009 Aug 13;460(7257):894-898
pubmed: 19633652
Nat Commun. 2016 Jun 17;7:11965
pubmed: 27311813
Science. 2018 Aug 3;361(6401):469-474
pubmed: 30072533
Genes (Basel). 2018 Jul 12;9(7):
pubmed: 30002345
Proc Natl Acad Sci U S A. 2013 Jan 15;110(3):E193-201
pubmed: 23277561
Proc Natl Acad Sci U S A. 2018 Dec 18;115(51):E11951-E11960
pubmed: 30510004
Nat Ecol Evol. 2021 Jul;5(7):1011-1023
pubmed: 33986540
Theor Popul Biol. 2008 Mar;73(2):257-63
pubmed: 18221761
Curr Biol. 2019 May 6;29(9):1528-1535.e6
pubmed: 31031118
ISME J. 2016 Nov;10(11):2557-2568
pubmed: 27022995
Evolution. 1974 Dec;28(4):527-545
pubmed: 28564821
Nature. 2019 Oct;574(7779):549-552
pubmed: 31645729
Nature. 2002 Feb 7;415(6872):644-6
pubmed: 11832946