---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '23090'
abstract:
- lang: eng
text: 'Homologous recombination is ubiquitous across evolution, generating variation
through genetic reshuffling. Although bacteria lack meiotic recombination, homologous
recombination has been known to extensively shape their genomes. However, the
mechanisms and ecological conditions sustaining frequent recombination in bacteria
remain unclear. Using an Escherichia coli–P1 phage model system, we reveal how
frequent recombination emerges from CRISPR-based herd immunity to a generalized
transducing phage (DNA vector). Herd immunity maintains phage-susceptible donor
bacteria, recipient immune bacteria, and transducing phage, which promotes chromosomal
gene flow that exceeds spontaneous mutation by up to two orders of magnitude.
Notably, recombination begins as bacterial cultures enter stationary phase, when
canonical mutation supply through population growth and DNA replication is strongly
reduced, and recombination can be reinitiated by brief fresh nutrient pulses.
Genetic analysis showed that stationary-phase recombination requires recA, recB,
and recG, connecting this process to a defined homologous recombination pathway,
and suggests a plausible transcriptional regulatory link to transition to nutrient
limitation. Bacterial herd immunity therefore has an unexpected evolutionary consequence:
it can promote homologous recombination by turning phages into de facto pollinators.
This mechanism can help explain how high rates of homologous recombination may
be sustained across bacterial populations and suggests that bacterial immune systems
can shape molecular evolution not only by blocking infection but also by regulating
genetic exchange.'
acknowledgement: We thank Stuart Baird, Nick Barton, Max Joesch, Meriem El Karoui,
Mato Lagator, Ivana Mašlaňová, Stepan Ovchinnikov, Roman Pantůček, Maroš Pleška,
Jitka Polechová, and Bryan Wu for their feedback on the manuscript. We are grateful
to the Redlinger Hut for hosting many discussions about the project away from the
daily buzz. We acknowledge the core facility CELLIM supported by the Czech-BioImaging
large RI project (LM2023050 funded by MEYS CR) for their support. This work was
supported by H2020 European Research Council EVOLHGT No. 648440 to JPB, European
Commission Programme EXCELES project LX22NPO5103 “National Institute of Virology
and Bacteriology” to PPl, and a bilateral Czech-Austrian mobility grant 8J3AT003
funded by MEYS CR and OeAD AT to PPa and CCG.
article_number: msag238
article_processing_charge: Yes
article_type: original
author:
- first_name: Pavel
full_name: Payne, Pavel
id: 35F78294-F248-11E8-B48F-1D18A9856A87
last_name: Payne
orcid: 0000-0002-2711-9453
- first_name: Pavel
full_name: Plevka, Pavel
last_name: Plevka
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Payne P, Plevka P, Bollback JP, Guet CC. Herd immunity underlies homologous
recombination in stationary phase bacteria. Molecular Biology and Evolution.
2026;43(10). doi:10.1093/molbev/msag238
apa: Payne, P., Plevka, P., Bollback, J. P., & Guet, C. C. (2026). Herd immunity
underlies homologous recombination in stationary phase bacteria. Molecular
Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msag238
chicago: Payne, Pavel, Pavel Plevka, Jonathan P Bollback, and Calin C Guet. “Herd
Immunity Underlies Homologous Recombination in Stationary Phase Bacteria.” Molecular
Biology and Evolution. Oxford University Press, 2026. https://doi.org/10.1093/molbev/msag238.
ieee: P. Payne, P. Plevka, J. P. Bollback, and C. C. Guet, “Herd immunity underlies
homologous recombination in stationary phase bacteria,” Molecular Biology and
Evolution, vol. 43, no. 10. Oxford University Press, 2026.
ista: Payne P, Plevka P, Bollback JP, Guet CC. 2026. Herd immunity underlies homologous
recombination in stationary phase bacteria. Molecular Biology and Evolution. 43(10),
msag238.
mla: Payne, Pavel, et al. “Herd Immunity Underlies Homologous Recombination in Stationary
Phase Bacteria.” Molecular Biology and Evolution, vol. 43, no. 10, msag238,
Oxford University Press, 2026, doi:10.1093/molbev/msag238.
short: P. Payne, P. Plevka, J.P. Bollback, C.C. Guet, Molecular Biology and Evolution
43 (2026).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: The data underlying this article are available in the article
and in its online material.
date_created: 2026-10-11T22:02:04Z
date_published: 2026-10-03T00:00:00Z
date_updated: 2026-10-12T10:51:54Z
day: '03'
ddc:
- '570'
department:
- _id: CaGu
doi: 10.1093/molbev/msag238
external_id:
pmid:
- '42827080'
fulldoi: https://doi.org/10.1093/molbev/msag238
has_accepted_license: '1'
intvolume: ' 43'
issue: '10'
keyword:
- homologous recombination
- defense systems
- CRISPR-Cas
- herd immunity
- stationary phase
- bacterial evolution
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1093/molbev/msag238
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: Molecular Biology and Evolution
publication_identifier:
eissn:
- 1537-1719
issn:
- 0737-4038
publication_status: epub_ahead
publisher: Oxford University Press
quality_controlled: '1'
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scopus_import: '1'
status: public
supplementarymaterial: yes
title: Herd immunity underlies homologous recombination in stationary phase bacteria
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type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 43
year: '2026'
...
---
_id: '9840'
abstract:
- lang: eng
text: Herd immunity, a process in which resistant individuals limit the spread of
a pathogen among susceptible hosts has been extensively studied in eukaryotes.
Even though bacteria have evolved multiple immune systems against their phage
pathogens, herd immunity in bacteria remains unexplored. Here we experimentally
demonstrate that herd immunity arises during phage epidemics in structured and
unstructured Escherichia coli populations consisting of differing frequencies
of susceptible and resistant cells harboring CRISPR immunity. In addition, we
develop a mathematical model that quantifies how herd immunity is affected by
spatial population structure, bacterial growth rate, and phage replication rate.
Using our model we infer a general epidemiological rule describing the relative
speed of an epidemic in partially resistant spatially structured populations.
Our experimental and theoretical findings indicate that herd immunity may be important
in bacterial communities, allowing for stable coexistence of bacteria and their
phages and the maintenance of polymorphism in bacterial immunity.
article_processing_charge: No
author:
- first_name: Pavel
full_name: Payne, Pavel
id: 35F78294-F248-11E8-B48F-1D18A9856A87
last_name: Payne
orcid: 0000-0002-2711-9453
- first_name: Lukas
full_name: Geyrhofer, Lukas
last_name: Geyrhofer
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: 'Payne P, Geyrhofer L, Barton NH, Bollback JP. Data from: CRISPR-based herd
immunity limits phage epidemics in bacterial populations. 2018. doi:10.5061/dryad.42n44'
apa: 'Payne, P., Geyrhofer, L., Barton, N. H., & Bollback, J. P. (2018). Data
from: CRISPR-based herd immunity limits phage epidemics in bacterial populations.
Dryad. https://doi.org/10.5061/dryad.42n44'
chicago: 'Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback.
“Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations.”
Dryad, 2018. https://doi.org/10.5061/dryad.42n44.'
ieee: 'P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “Data from: CRISPR-based
herd immunity limits phage epidemics in bacterial populations.” Dryad, 2018.'
ista: 'Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. Data from: CRISPR-based
herd immunity limits phage epidemics in bacterial populations, Dryad, 10.5061/dryad.42n44.'
mla: 'Payne, Pavel, et al. Data from: CRISPR-Based Herd Immunity Limits Phage
Epidemics in Bacterial Populations. Dryad, 2018, doi:10.5061/dryad.42n44.'
short: P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, (2018).
date_created: 2021-08-09T13:10:02Z
date_published: 2018-03-12T00:00:00Z
date_updated: 2025-04-15T08:17:50Z
day: '12'
department:
- _id: NiBa
- _id: JoBo
doi: 10.5061/dryad.42n44
fulldoi: https://doi.org/10.5061/dryad.42n44
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month: '03'
oa: 1
oa_version: Published Version
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title: 'Data from: CRISPR-based herd immunity limits phage epidemics in bacterial
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---
_id: '423'
abstract:
- lang: eng
text: Herd immunity, a process in which resistant individuals limit the spread of
a pathogen among susceptible hosts has been extensively studied in eukaryotes.
Even though bacteria have evolved multiple immune systems against their phage
pathogens, herd immunity in bacteria remains unexplored. Here we experimentally
demonstrate that herd immunity arises during phage epidemics in structured and
unstructured Escherichia coli populations consisting of differing frequencies
of susceptible and resistant cells harboring CRISPR immunity. In addition, we
develop a mathematical model that quantifies how herd immunity is affected by
spatial population structure, bacterial growth rate, and phage replication rate.
Using our model we infer a general epidemiological rule describing the relative
speed of an epidemic in partially resistant spatially structured populations.
Our experimental and theoretical findings indicate that herd immunity may be important
in bacterial communities, allowing for stable coexistence of bacteria and their
phages and the maintenance of polymorphism in bacterial immunity.
acknowledgement: "We are grateful to Remy Chait for his help and assistance with establishing
our experimental setups and to Tobias Bergmiller for valuable insights into some
specific experimental details. We thank Luciano Marraffini for donating us the pCas9
plasmid used in this study. We also want to express our gratitude to Seth Barribeau,
Andrea Betancourt, Călin Guet, Mato Lagator, Tiago Paixão and Maroš Pleška for valuable
discussions on the manuscript. Finally, we would like to thank the \r\neditors and
reviewers for their helpful comments and suggestions."
article_number: e32035
article_processing_charge: No
author:
- first_name: Pavel
full_name: Payne, Pavel
id: 35F78294-F248-11E8-B48F-1D18A9856A87
last_name: Payne
orcid: 0000-0002-2711-9453
- first_name: Lukas
full_name: Geyrhofer, Lukas
last_name: Geyrhofer
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: Payne P, Geyrhofer L, Barton NH, Bollback JP. CRISPR-based herd immunity can
limit phage epidemics in bacterial populations. eLife. 2018;7. doi:10.7554/eLife.32035
apa: Payne, P., Geyrhofer, L., Barton, N. H., & Bollback, J. P. (2018). CRISPR-based
herd immunity can limit phage epidemics in bacterial populations. ELife.
eLife Sciences Publications. https://doi.org/10.7554/eLife.32035
chicago: Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback.
“CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.”
ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.32035.
ieee: P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “CRISPR-based herd
immunity can limit phage epidemics in bacterial populations,” eLife, vol.
7. eLife Sciences Publications, 2018.
ista: Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. CRISPR-based herd immunity
can limit phage epidemics in bacterial populations. eLife. 7, e32035.
mla: Payne, Pavel, et al. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics
in Bacterial Populations.” ELife, vol. 7, e32035, eLife Sciences Publications,
2018, doi:10.7554/eLife.32035.
short: P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, ELife 7 (2018).
date_created: 2018-12-11T11:46:23Z
date_published: 2018-03-09T00:00:00Z
date_updated: 2025-03-31T16:00:24Z
day: '09'
ddc:
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department:
- _id: NiBa
- _id: JoBo
doi: 10.7554/eLife.32035
ec_funded: 1
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project:
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call_identifier: H2020
grant_number: '648440'
name: Selective Barriers to Horizontal Gene Transfer
publication: eLife
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title: CRISPR-based herd immunity can limit phage epidemics in bacterial populations
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
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year: '2018'
...
---
OA_place: publisher
_id: '6291'
abstract:
- lang: eng
text: Bacteria and their pathogens – phages – are the most abundant living entities
on Earth. Throughout their coevolution, bacteria have evolved multiple immune
systems to overcome the ubiquitous threat from the phages. Although the molecu-
lar details of these immune systems’ functions are relatively well understood,
their epidemiological consequences for the phage-bacterial communities have been
largely neglected. In this thesis we employed both experimental and theoretical
methods to explore whether herd and social immunity may arise in bacterial popu-
lations. Using our experimental system consisting of Escherichia coli strains
with a CRISPR based immunity to the T7 phage we show that herd immunity arises
in phage-bacterial communities and that it is accentuated when the populations
are spatially structured. By fitting a mathematical model, we inferred expressions
for the herd immunity threshold and the velocity of spread of a phage epidemic
in partially resistant bacterial populations, which both depend on the bacterial
growth rate, phage burst size and phage latent period. We also investigated the
poten- tial for social immunity in Streptococcus thermophilus and its phage 2972
using a bioinformatic analysis of potentially coding short open reading frames
with a signalling signature, encoded within the CRISPR associated genes. Subsequently,
we tested one identified potentially signalling peptide and found that its addition
to a phage-challenged culture increases probability of survival of bacteria two
fold, although the results were only marginally significant. Together, these results
demonstrate that the ubiquitous arms races between bacteria and phages have further
consequences at the level of the population.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Pavel
full_name: Payne, Pavel
id: 35F78294-F248-11E8-B48F-1D18A9856A87
last_name: Payne
orcid: 0000-0002-2711-9453
citation:
ama: Payne P. Bacterial herd and social immunity to phages. 2017.
apa: Payne, P. (2017). Bacterial herd and social immunity to phages. Institute
of Science and Technology Austria.
chicago: Payne, Pavel. “Bacterial Herd and Social Immunity to Phages.” Institute
of Science and Technology Austria, 2017.
ieee: P. Payne, “Bacterial herd and social immunity to phages,” Institute of Science
and Technology Austria, 2017.
ista: Payne P. 2017. Bacterial herd and social immunity to phages. Institute of
Science and Technology Austria.
mla: Payne, Pavel. Bacterial Herd and Social Immunity to Phages. Institute
of Science and Technology Austria, 2017.
short: P. Payne, Bacterial Herd and Social Immunity to Phages, Institute of Science
and Technology Austria, 2017.
corr_author: '1'
date_created: 2019-04-09T15:16:45Z
date_published: 2017-02-01T00:00:00Z
date_updated: 2026-04-08T14:16:28Z
day: '01'
ddc:
- '570'
degree_awarded: PhD
department:
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- _id: JoBo
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language:
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month: '02'
oa: 1
oa_version: Published Version
page: '83'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: Bacterial herd and social immunity to phages
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2017'
...