Horizontal Gene Transfer and CRISPR Targeting Drive Phage-Bacterial Host Interactions and Coevolution in "Pink Berry" Marine Microbial Aggregates.
CRISPR
horizontal gene transfer
metagenomics
microbial ecology
microbial evolution
phage
viromics
Journal
Applied and environmental microbiology
ISSN: 1098-5336
Titre abrégé: Appl Environ Microbiol
Pays: United States
ID NLM: 7605801
Informations de publication
Date de publication:
26 07 2023
26 07 2023
Historique:
medline:
27
7
2023
pubmed:
5
7
2023
entrez:
5
7
2023
Statut:
ppublish
Résumé
Bacteriophages (phages), which are viruses that infect bacteria, are the most abundant components of microbial communities and play roles in community dynamics and host evolution. However, the study of phage-host interactions is hindered by a paucity of model systems from natural environments. Here, we investigate phage-host interactions in the "pink berry" consortia, which are naturally occurring, low-diversity, macroscopic bacterial aggregates that are found in the Sippewissett Salt Marsh (Falmouth, MA, USA). We leverage metagenomic sequence data and a comparative genomics approach to identify eight compete phage genomes, infer their bacterial hosts from host-encoded clustered regularly interspaced short palindromic repeats (CRISPRs), and observe the potential evolutionary consequences of these interactions. Seven of the eight phages identified infect known pink berry symbionts, namely,
Identifiants
pubmed: 37404190
doi: 10.1128/aem.00177-23
pmc: PMC10370329
doi:
Types de publication
Case Reports
Journal Article
Research Support, U.S. Gov't, Non-P.H.S.
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0017723Subventions
Organisme : HHS | National Institutes of Health (NIH)
ID : T32 DK077653-29
Commentaires et corrections
Type : UpdateOf
Déclaration de conflit d'intérêts
The authors declare no conflict of interest.
Références
Bioinformatics. 2020 Aug 15;36(14):4126-4129
pubmed: 32413137
Nucleic Acids Res. 2013 Sep;41(17):8034-44
pubmed: 23863837
CRISPR J. 2021 Aug;4(4):558-574
pubmed: 34406047
Curr Protoc Bioinformatics. 2014 Sep 08;47:8.13.1-24
pubmed: 25199793
Viruses. 2021 Mar 18;13(3):
pubmed: 33803862
Microbiome. 2022 Aug 27;10(1):137
pubmed: 36028909
Mol Microbiol. 2000 Apr;36(1):244-6
pubmed: 10760181
Sci Rep. 2017 Aug 15;7(1):8292
pubmed: 28811656
Environ Microbiol. 2020 Dec;22(12):4919-4933
pubmed: 32935433
Nucleic Acids Res. 2016 Jan 4;44(D1):D733-45
pubmed: 26553804
Nat Biotechnol. 2019 Jun;37(6):632-639
pubmed: 31061483
Mol Microbiol. 2002 Mar;43(6):1565-75
pubmed: 11952905
Environ Microbiol. 2013 Feb;15(2):463-70
pubmed: 23057534
Nature. 1989 Aug 10;340(6233):467-8
pubmed: 2755508
J Bacteriol. 2008 Feb;190(4):1390-400
pubmed: 18065545
Nucleic Acids Res. 2021 Jan 8;49(D1):D1020-D1028
pubmed: 33270901
Environ Microbiol. 2014 Nov;16(11):3398-415
pubmed: 24428801
Nature. 2020 Jan;577(7790):327-336
pubmed: 31942051
Science. 2015 May 22;348(6237):1261498
pubmed: 25999515
Nat Protoc. 2015 Jun;10(6):845-58
pubmed: 25950237
Microbiome. 2020 Jun 10;8(1):90
pubmed: 32522236
Bioinformatics. 2011 Apr 1;27(7):1017-8
pubmed: 21330290
Microbiol Rev. 1983 Sep;47(3):345-60
pubmed: 6314109
Microbiology (Reading). 2009 Mar;155(Pt 3):733-740
pubmed: 19246744
CRISPR J. 2023 Jul 17;:
pubmed: 37459160
Science. 2008 May 23;320(5879):1047-50
pubmed: 18497291
Microbiome. 2020 Nov 15;8(1):158
pubmed: 33190645
NAR Genom Bioinform. 2021 Aug 05;3(3):lqab067
pubmed: 34377978
BMC Bioinformatics. 2007 Jun 18;8:209
pubmed: 17577412
mSystems. 2018 Oct 23;3(5):
pubmed: 30374457
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Appl Environ Microbiol. 2013 Dec;79(24):7547-55
pubmed: 24123737
Bioinformatics. 2023 Jan 1;39(1):
pubmed: 36453861
Science. 2007 Mar 23;315(5819):1709-12
pubmed: 17379808
Gigascience. 2021 Feb 16;10(2):
pubmed: 33590861
Bioinformatics. 2019 Nov 1;35(22):4537-4542
pubmed: 31329826
Science. 2010 Jan 8;327(5962):167-70
pubmed: 20056882
Nat Commun. 2021 Jun 9;12(1):3503
pubmed: 34108477
Nucleic Acids Res. 2013 May 1;41(10):e105
pubmed: 23511966
Bioinformatics. 2017 Nov 01;33(21):3340-3347
pubmed: 29077810
PeerJ. 2021 May 6;9:e11396
pubmed: 33996289
PLoS Comput Biol. 2011 Oct;7(10):e1002195
pubmed: 22039361
Genome Res. 2004 Jun;14(6):1188-90
pubmed: 15173120
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
Genome Biol. 2007;8(4):R61
pubmed: 17442114
Z Naturforsch C Biosci. 1983 Mar-Apr;38(3-4):294-6
pubmed: 6346725
Nucleic Acids Res. 2022 Jan 7;50(D1):D161-D164
pubmed: 34850943
ISME J. 2022 Aug;16(8):1921-1931
pubmed: 35459792
Curr Biol. 2022 Jan 10;32(1):220-227.e5
pubmed: 34758284
Nucleic Acids Res. 1990 Oct 25;18(20):6097-100
pubmed: 2172928
Nucleic Acids Res. 2021 Jan 8;49(D1):D412-D419
pubmed: 33125078
Int J Syst Evol Microbiol. 2007 Jan;57(Pt 1):81-91
pubmed: 17220447
Genome Res. 2004 Jul;14(7):1394-403
pubmed: 15231754
Environ Microbiol. 2009 Feb;11(2):457-66
pubmed: 19196276
Nat Microbiol. 2018 Jul;3(7):754-766
pubmed: 29867096
Ann Rev Mar Sci. 2014;6:393-414
pubmed: 23987913
Science. 2012 Aug 17;337(6096):816-21
pubmed: 22745249
PLoS One. 2014 Jul 07;9(7):e101710
pubmed: 25000306
Genome Res. 2011 Oct;21(10):1616-25
pubmed: 21880779
FEMS Microbiol Rev. 2014 Sep;38(5):916-31
pubmed: 24617569
Nucleic Acids Res. 2015 Jan;43(Database issue):D571-7
pubmed: 25428358
Cell Rep. 2020 Sep 15;32(11):108142
pubmed: 32937127
Bioinformatics. 2021 Aug 25;37(16):2473-2475
pubmed: 33459763
Philos Trans R Soc Lond B Biol Sci. 2017 Dec 5;372(1735):
pubmed: 29061896
PeerJ. 2017 Sep 21;5:e3817
pubmed: 28948103
Science. 2014 May 16;344(6185):757-60
pubmed: 24789974
Mol Ecol Resour. 2017 Jan;17(1):44-53
pubmed: 27401132
Brief Bioinform. 2013 Mar;14(2):178-92
pubmed: 22517427
BMC Bioinformatics. 2009 Dec 15;10:421
pubmed: 20003500
J Mol Biol. 1990 Oct 5;215(3):403-10
pubmed: 2231712