Aquaculture as a source of empirical evidence for coevolution between CRISPR-Cas and phage

Ville Hoikkala, Gabriel M. F. Almeida, Elina Laanto, Lotta-Riina Sundberg

Tutkimustuotos: ArtikkelijulkaisuKatsausartikkeliTieteellinenvertaisarvioitu

Kuvaus

So far, studies on the bacterial immune system CRISPR-Cas and its ecological and evolutionary effects have been largely limited to laboratory conditions. While providing crucial information on the constituents of CRISPR-Cas, such studies may overlook fundamental components that affect bacterial immunity in natural habitats. Translating laboratory-derived predictions to nature is not a trivial task, owing partly to the instability of natural communities and difficulties in repeated sampling. To this end, we review how aquaculture, the farming of fishes and other aquatic species, may provide suitable semi-natural laboratories for examining the role of CRISPR-Cas in phage/bacterium coevolution. Existing data from disease surveillance conducted in aquaculture, coupled with growing interest towards phage therapy, may have already resulted in large collections of bacterium and phage isolates. These data, combined with premeditated efforts, can provide empirical evidence on phage-bacterium dynamics such as the bacteriophage adherence to mucus hypothesis, phage life cycles and their relationship with CRISPR-Cas and other immune defences. Typing of CRISPR spacer content in pathogenic bacteria can also provide practical information on diversity and origin of isolates during outbreaks. In addition to providing information of CRISPR functionality and phage-bacterium dynamics, aquaculture systems can significantly impact perspectives on design of phage-based disease treatment at the current era of increasing antibiotic resistance.

This article is part of a discussion meeting issue 'The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems'.
Alkuperäiskielienglanti
Artikkeli20180100
LehtiPhilosophical Transactions of the Royal Society. Biological Sciences
Vuosikerta374
Numero1772
Sivumäärä8
ISSN0962-8436
DOI - pysyväislinkit
TilaJulkaistu - 13 toukokuuta 2019
Julkaistu ulkoisestiKyllä
OKM-julkaisutyyppiA2 Katsausartikkeli tieteellisessä aikakauslehdessä

Tieteenalat

  • 1181 Ekologia, evoluutiobiologia
  • 1182 Biokemia, solu- ja molekyylibiologia

Lainaa tätä

Hoikkala, Ville ; Almeida, Gabriel M. F. ; Laanto, Elina ; Sundberg, Lotta-Riina. / Aquaculture as a source of empirical evidence for coevolution between CRISPR-Cas and phage. Julkaisussa: Philosophical Transactions of the Royal Society. Biological Sciences. 2019 ; Vuosikerta 374, Nro 1772.
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title = "Aquaculture as a source of empirical evidence for coevolution between CRISPR-Cas and phage",
abstract = "So far, studies on the bacterial immune system CRISPR-Cas and its ecological and evolutionary effects have been largely limited to laboratory conditions. While providing crucial information on the constituents of CRISPR-Cas, such studies may overlook fundamental components that affect bacterial immunity in natural habitats. Translating laboratory-derived predictions to nature is not a trivial task, owing partly to the instability of natural communities and difficulties in repeated sampling. To this end, we review how aquaculture, the farming of fishes and other aquatic species, may provide suitable semi-natural laboratories for examining the role of CRISPR-Cas in phage/bacterium coevolution. Existing data from disease surveillance conducted in aquaculture, coupled with growing interest towards phage therapy, may have already resulted in large collections of bacterium and phage isolates. These data, combined with premeditated efforts, can provide empirical evidence on phage-bacterium dynamics such as the bacteriophage adherence to mucus hypothesis, phage life cycles and their relationship with CRISPR-Cas and other immune defences. Typing of CRISPR spacer content in pathogenic bacteria can also provide practical information on diversity and origin of isolates during outbreaks. In addition to providing information of CRISPR functionality and phage-bacterium dynamics, aquaculture systems can significantly impact perspectives on design of phage-based disease treatment at the current era of increasing antibiotic resistance.This article is part of a discussion meeting issue 'The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems'.",
keywords = "CRISPR, aquaculture, ecology, coevolution, bacteria, phage, HORIZONTAL TRANSFER, MYCOBACTERIUM-TUBERCULOSIS, EVOLUTIONARY DYNAMICS, ACQUIRED-RESISTANCE, VIRULENCE FACTORS, SYSTEMS, REPEATS, ECOLOGY, GENES, DNA, 1181 Ecology, evolutionary biology, 1182 Biochemistry, cell and molecular biology",
author = "Ville Hoikkala and Almeida, {Gabriel M. F.} and Elina Laanto and Lotta-Riina Sundberg",
year = "2019",
month = "5",
day = "13",
doi = "10.1098/rstb.2018.0100",
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journal = "Philosophical Transactions of the Royal Society. Biological Sciences",
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Aquaculture as a source of empirical evidence for coevolution between CRISPR-Cas and phage. / Hoikkala, Ville; Almeida, Gabriel M. F.; Laanto, Elina; Sundberg, Lotta-Riina.

julkaisussa: Philosophical Transactions of the Royal Society. Biological Sciences, Vuosikerta 374, Nro 1772, 20180100, 13.05.2019.

Tutkimustuotos: ArtikkelijulkaisuKatsausartikkeliTieteellinenvertaisarvioitu

TY - JOUR

T1 - Aquaculture as a source of empirical evidence for coevolution between CRISPR-Cas and phage

AU - Hoikkala, Ville

AU - Almeida, Gabriel M. F.

AU - Laanto, Elina

AU - Sundberg, Lotta-Riina

PY - 2019/5/13

Y1 - 2019/5/13

N2 - So far, studies on the bacterial immune system CRISPR-Cas and its ecological and evolutionary effects have been largely limited to laboratory conditions. While providing crucial information on the constituents of CRISPR-Cas, such studies may overlook fundamental components that affect bacterial immunity in natural habitats. Translating laboratory-derived predictions to nature is not a trivial task, owing partly to the instability of natural communities and difficulties in repeated sampling. To this end, we review how aquaculture, the farming of fishes and other aquatic species, may provide suitable semi-natural laboratories for examining the role of CRISPR-Cas in phage/bacterium coevolution. Existing data from disease surveillance conducted in aquaculture, coupled with growing interest towards phage therapy, may have already resulted in large collections of bacterium and phage isolates. These data, combined with premeditated efforts, can provide empirical evidence on phage-bacterium dynamics such as the bacteriophage adherence to mucus hypothesis, phage life cycles and their relationship with CRISPR-Cas and other immune defences. Typing of CRISPR spacer content in pathogenic bacteria can also provide practical information on diversity and origin of isolates during outbreaks. In addition to providing information of CRISPR functionality and phage-bacterium dynamics, aquaculture systems can significantly impact perspectives on design of phage-based disease treatment at the current era of increasing antibiotic resistance.This article is part of a discussion meeting issue 'The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems'.

AB - So far, studies on the bacterial immune system CRISPR-Cas and its ecological and evolutionary effects have been largely limited to laboratory conditions. While providing crucial information on the constituents of CRISPR-Cas, such studies may overlook fundamental components that affect bacterial immunity in natural habitats. Translating laboratory-derived predictions to nature is not a trivial task, owing partly to the instability of natural communities and difficulties in repeated sampling. To this end, we review how aquaculture, the farming of fishes and other aquatic species, may provide suitable semi-natural laboratories for examining the role of CRISPR-Cas in phage/bacterium coevolution. Existing data from disease surveillance conducted in aquaculture, coupled with growing interest towards phage therapy, may have already resulted in large collections of bacterium and phage isolates. These data, combined with premeditated efforts, can provide empirical evidence on phage-bacterium dynamics such as the bacteriophage adherence to mucus hypothesis, phage life cycles and their relationship with CRISPR-Cas and other immune defences. Typing of CRISPR spacer content in pathogenic bacteria can also provide practical information on diversity and origin of isolates during outbreaks. In addition to providing information of CRISPR functionality and phage-bacterium dynamics, aquaculture systems can significantly impact perspectives on design of phage-based disease treatment at the current era of increasing antibiotic resistance.This article is part of a discussion meeting issue 'The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems'.

KW - CRISPR

KW - aquaculture

KW - ecology

KW - coevolution

KW - bacteria

KW - phage

KW - HORIZONTAL TRANSFER

KW - MYCOBACTERIUM-TUBERCULOSIS

KW - EVOLUTIONARY DYNAMICS

KW - ACQUIRED-RESISTANCE

KW - VIRULENCE FACTORS

KW - SYSTEMS

KW - REPEATS

KW - ECOLOGY

KW - GENES

KW - DNA

KW - 1181 Ecology, evolutionary biology

KW - 1182 Biochemistry, cell and molecular biology

U2 - 10.1098/rstb.2018.0100

DO - 10.1098/rstb.2018.0100

M3 - Review Article

VL - 374

JO - Philosophical Transactions of the Royal Society. Biological Sciences

JF - Philosophical Transactions of the Royal Society. Biological Sciences

SN - 0962-8436

IS - 1772

M1 - 20180100

ER -