---
_id: '822'
abstract:
- lang: eng
text: 'Polymicrobial infections constitute small ecosystems that accommodate several
bacterial species. Commonly, these bacteria are investigated in isolation. However,
it is unknown to what extent the isolates interact and whether their interactions
alter bacterial growth and ecosystem resilience in the presence and absence of
antibiotics. We quantified the complete ecological interaction network for 72
bacterial isolates collected from 23 individuals diagnosed with polymicrobial
urinary tract infections and found that most interactions cluster based on evolutionary
relatedness. Statistical network analysis revealed that competitive and cooperative
reciprocal interactions are enriched in the global network, while cooperative
interactions are depleted in the individual host community networks. A population
dynamics model parameterized by our measurements suggests that interactions restrict
community stability, explaining the observed species diversity of these communities.
We further show that the clinical isolates frequently protect each other from
clinically relevant antibiotics. Together, these results highlight that ecological
interactions are crucial for the growth and survival of bacteria in polymicrobial
infection communities and affect their assembly and resilience. '
article_processing_charge: No
author:
- first_name: Marjon
full_name: De Vos, Marjon
id: 3111FFAC-F248-11E8-B48F-1D18A9856A87
last_name: De Vos
- first_name: Marcin P
full_name: Zagórski, Marcin P
id: 343DA0DC-F248-11E8-B48F-1D18A9856A87
last_name: Zagórski
orcid: 0000-0001-7896-7762
- first_name: Alan
full_name: Mcnally, Alan
last_name: Mcnally
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: de Vos M, Zagórski MP, Mcnally A, Bollenbach MT. Interaction networks, ecological
stability, and collective antibiotic tolerance in polymicrobial infections. PNAS.
2017;114(40):10666-10671. doi:10.1073/pnas.1713372114
apa: de Vos, M., Zagórski, M. P., Mcnally, A., & Bollenbach, M. T. (2017). Interaction
networks, ecological stability, and collective antibiotic tolerance in polymicrobial
infections. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1713372114
chicago: Vos, Marjon de, Marcin P Zagórski, Alan Mcnally, and Mark Tobias Bollenbach.
“Interaction Networks, Ecological Stability, and Collective Antibiotic Tolerance
in Polymicrobial Infections.” PNAS. National Academy of Sciences, 2017.
https://doi.org/10.1073/pnas.1713372114.
ieee: M. de Vos, M. P. Zagórski, A. Mcnally, and M. T. Bollenbach, “Interaction
networks, ecological stability, and collective antibiotic tolerance in polymicrobial
infections,” PNAS, vol. 114, no. 40. National Academy of Sciences, pp.
10666–10671, 2017.
ista: de Vos M, Zagórski MP, Mcnally A, Bollenbach MT. 2017. Interaction networks,
ecological stability, and collective antibiotic tolerance in polymicrobial infections.
PNAS. 114(40), 10666–10671.
mla: de Vos, Marjon, et al. “Interaction Networks, Ecological Stability, and Collective
Antibiotic Tolerance in Polymicrobial Infections.” PNAS, vol. 114, no.
40, National Academy of Sciences, 2017, pp. 10666–71, doi:10.1073/pnas.1713372114.
short: M. de Vos, M.P. Zagórski, A. Mcnally, M.T. Bollenbach, PNAS 114 (2017) 10666–10671.
date_created: 2018-12-11T11:48:41Z
date_published: 2017-10-03T00:00:00Z
date_updated: 2023-09-26T16:18:48Z
day: '03'
department:
- _id: ToBo
doi: 10.1073/pnas.1713372114
ec_funded: 1
external_id:
isi:
- '000412130500061'
pmid:
- '28923953'
intvolume: ' 114'
isi: 1
issue: '40'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5635929/
month: '10'
oa: 1
oa_version: Submitted Version
page: 10666 - 10671
pmid: 1
project:
- _id: 25E83C2C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303507'
name: Optimality principles in responses to antibiotics
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
publication: PNAS
publication_identifier:
issn:
- '00278424'
publication_status: published
publisher: National Academy of Sciences
publist_id: '6827'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Interaction networks, ecological stability, and collective antibiotic tolerance
in polymicrobial infections
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 114
year: '2017'
...
---
_id: '1571'
abstract:
- lang: eng
text: Epistatic interactions can frustrate and shape evolutionary change. Indeed,
phenotypes may fail to evolve when essential mutations are only accessible through
positive selection if they are fixed simultaneously. How environmental variability
affects such constraints is poorly understood. Here, we studied genetic constraints
in fixed and fluctuating environments using the Escherichia coli lac operon as
a model system for genotype-environment interactions. We found that, in different
fixed environments, all trajectories that were reconstructed by applying point
mutations within the transcription factor-operator interface became trapped at
suboptima, where no additional improvements were possible. Paradoxically, repeated
switching between these same environments allows unconstrained adaptation by continuous
improvements. This evolutionary mode is explained by pervasive cross-environmental
tradeoffs that reposition the peaks in such a way that trapped genotypes can repeatedly
climb ascending slopes and hence, escape adaptive stasis. Using a Markov approach,
we developed a mathematical framework to quantify the landscape-crossing rates
and show that this ratchet-like adaptive mechanism is robust in a wide spectrum
of fluctuating environments. Overall, this study shows that genetic constraints
can be overcome by environmental change and that crossenvironmental tradeoffs
do not necessarily impede but also, can facilitate adaptive evolution. Because
tradeoffs and environmental variability are ubiquitous in nature, we speculate
this evolutionary mode to be of general relevance.
acknowledgement: This work is part of the research program of the Foundation for Fundamental
Research on Matter, which is part of the Netherlands Organization for Scientific
Research (NWO). M.G.J.d.V. was (partially) funded by NWO Earth and Life Sciences
(ALW), project 863.14.015. We thank D. M. Weinreich, J. A. G. M. de Visser, T. Paixão,
J. Polechová, T. Friedlander, and A. E. Mayo for reading and commenting on earlier
versions of the manuscript and B. Houchmandzadeh, O. Rivoire, and M. Hemery for
discussions and suggestions on the Markov computation. Furthermore, we thank F.
J. Poelwijk for sharing plasmid pCascade5 and pRD007 and Y. Yokobayashi for sharing
plasmid pINV-110. We also thank the anonymous reviewers for remarks on the initial
version of the manuscript.
author:
- first_name: Marjon
full_name: De Vos, Marjon
id: 3111FFAC-F248-11E8-B48F-1D18A9856A87
last_name: De Vos
- first_name: Alexandre
full_name: Dawid, Alexandre
last_name: Dawid
- first_name: Vanda
full_name: Šunderlíková, Vanda
last_name: Šunderlíková
- first_name: Sander
full_name: Tans, Sander
last_name: Tans
citation:
ama: de Vos M, Dawid A, Šunderlíková V, Tans S. Breaking evolutionary constraint
with a tradeoff ratchet. PNAS. 2015;112(48):14906-14911. doi:10.1073/pnas.1510282112
apa: de Vos, M., Dawid, A., Šunderlíková, V., & Tans, S. (2015). Breaking evolutionary
constraint with a tradeoff ratchet. PNAS. National Academy of Sciences.
https://doi.org/10.1073/pnas.1510282112
chicago: Vos, Marjon de, Alexandre Dawid, Vanda Šunderlíková, and Sander Tans. “Breaking
Evolutionary Constraint with a Tradeoff Ratchet.” PNAS. National Academy
of Sciences, 2015. https://doi.org/10.1073/pnas.1510282112.
ieee: M. de Vos, A. Dawid, V. Šunderlíková, and S. Tans, “Breaking evolutionary
constraint with a tradeoff ratchet,” PNAS, vol. 112, no. 48. National Academy
of Sciences, pp. 14906–14911, 2015.
ista: de Vos M, Dawid A, Šunderlíková V, Tans S. 2015. Breaking evolutionary constraint
with a tradeoff ratchet. PNAS. 112(48), 14906–14911.
mla: de Vos, Marjon, et al. “Breaking Evolutionary Constraint with a Tradeoff Ratchet.”
PNAS, vol. 112, no. 48, National Academy of Sciences, 2015, pp. 14906–11,
doi:10.1073/pnas.1510282112.
short: M. de Vos, A. Dawid, V. Šunderlíková, S. Tans, PNAS 112 (2015) 14906–14911.
date_created: 2018-12-11T11:52:47Z
date_published: 2015-12-01T00:00:00Z
date_updated: 2021-01-12T06:51:40Z
day: '01'
department:
- _id: ToBo
doi: 10.1073/pnas.1510282112
intvolume: ' 112'
issue: '48'
language:
- iso: eng
month: '12'
oa_version: None
page: 14906 - 14911
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '5600'
quality_controlled: '1'
scopus_import: 1
status: public
title: Breaking evolutionary constraint with a tradeoff ratchet
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2015'
...
---
_id: '2220'
abstract:
- lang: eng
text: In this issue of Chemistry & Biology, Cokol and colleagues report a systematic
study of drug interactions between antifungal compounds. Suppressive drug interactions
occur more frequently than previously realized and come in different flavors with
interesting implications.
author:
- first_name: Marjon
full_name: De Vos, Marjon
id: 3111FFAC-F248-11E8-B48F-1D18A9856A87
last_name: De Vos
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: de Vos M, Bollenbach MT. Suppressive drug interactions between antifungals.
Chemistry and Biology. 2014;21(4):439-440. doi:10.1016/j.chembiol.2014.04.004
apa: de Vos, M., & Bollenbach, M. T. (2014). Suppressive drug interactions between
antifungals. Chemistry and Biology. Cell Press. https://doi.org/10.1016/j.chembiol.2014.04.004
chicago: Vos, Marjon de, and Mark Tobias Bollenbach. “Suppressive Drug Interactions
between Antifungals.” Chemistry and Biology. Cell Press, 2014. https://doi.org/10.1016/j.chembiol.2014.04.004.
ieee: M. de Vos and M. T. Bollenbach, “Suppressive drug interactions between antifungals,”
Chemistry and Biology, vol. 21, no. 4. Cell Press, pp. 439–440, 2014.
ista: de Vos M, Bollenbach MT. 2014. Suppressive drug interactions between antifungals.
Chemistry and Biology. 21(4), 439–440.
mla: de Vos, Marjon, and Mark Tobias Bollenbach. “Suppressive Drug Interactions
between Antifungals.” Chemistry and Biology, vol. 21, no. 4, Cell Press,
2014, pp. 439–40, doi:10.1016/j.chembiol.2014.04.004.
short: M. de Vos, M.T. Bollenbach, Chemistry and Biology 21 (2014) 439–440.
date_created: 2018-12-11T11:56:24Z
date_published: 2014-04-24T00:00:00Z
date_updated: 2021-01-12T06:56:06Z
day: '24'
department:
- _id: ToBo
doi: 10.1016/j.chembiol.2014.04.004
external_id:
pmid:
- '24766845'
intvolume: ' 21'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/24766845
month: '04'
oa: 1
oa_version: Published Version
page: 439 - 440
pmid: 1
publication: Chemistry and Biology
publication_identifier:
issn:
- '10745521'
publication_status: published
publisher: Cell Press
publist_id: '4747'
quality_controlled: '1'
scopus_import: 1
status: public
title: Suppressive drug interactions between antifungals
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2014'
...
---
_id: '2810'
abstract:
- lang: eng
text: The epistatic interactions that underlie evolutionary constraint have mainly
been studied for constant external conditions. However, environmental changes
may modulate epistasis and hence affect genetic constraints. Here we investigate
genetic constraints in the adaptive evolution of a novel regulatory function in
variable environments, using the lac repressor, LacI, as a model system. We have
systematically reconstructed mutational trajectories from wild type LacI to three
different variants that each exhibit an inverse response to the inducing ligand
IPTG, and analyzed the higher-order interactions between genetic and environmental
changes. We find epistasis to depend strongly on the environment. As a result,
mutational steps essential to inversion but inaccessible by positive selection
in one environment, become accessible in another. We present a graphical method
to analyze the observed complex higher-order interactions between multiple mutations
and environmental change, and show how the interactions can be explained by a
combination of mutational effects on allostery and thermodynamic stability. This
dependency of genetic constraint on the environment should fundamentally affect
evolutionary dynamics and affects the interpretation of phylogenetic data.
article_number: e1003580
author:
- first_name: Marjon
full_name: De Vos, Marjon
id: 3111FFAC-F248-11E8-B48F-1D18A9856A87
last_name: De Vos
- first_name: Frank
full_name: Poelwijk, Frank
last_name: Poelwijk
- first_name: Nico
full_name: Battich, Nico
last_name: Battich
- first_name: Joseph
full_name: Ndika, Joseph
last_name: Ndika
- first_name: Sander
full_name: Tans, Sander
last_name: Tans
citation:
ama: de Vos M, Poelwijk F, Battich N, Ndika J, Tans S. Environmental dependence
of genetic constraint. PLoS Genetics. 2013;9(6). doi:10.1371/journal.pgen.1003580
apa: de Vos, M., Poelwijk, F., Battich, N., Ndika, J., & Tans, S. (2013). Environmental
dependence of genetic constraint. PLoS Genetics. Public Library of Science.
https://doi.org/10.1371/journal.pgen.1003580
chicago: Vos, Marjon de, Frank Poelwijk, Nico Battich, Joseph Ndika, and Sander
Tans. “Environmental Dependence of Genetic Constraint.” PLoS Genetics.
Public Library of Science, 2013. https://doi.org/10.1371/journal.pgen.1003580.
ieee: M. de Vos, F. Poelwijk, N. Battich, J. Ndika, and S. Tans, “Environmental
dependence of genetic constraint,” PLoS Genetics, vol. 9, no. 6. Public
Library of Science, 2013.
ista: de Vos M, Poelwijk F, Battich N, Ndika J, Tans S. 2013. Environmental dependence
of genetic constraint. PLoS Genetics. 9(6), e1003580.
mla: de Vos, Marjon, et al. “Environmental Dependence of Genetic Constraint.” PLoS
Genetics, vol. 9, no. 6, e1003580, Public Library of Science, 2013, doi:10.1371/journal.pgen.1003580.
short: M. de Vos, F. Poelwijk, N. Battich, J. Ndika, S. Tans, PLoS Genetics 9 (2013).
date_created: 2018-12-11T11:59:43Z
date_published: 2013-06-27T00:00:00Z
date_updated: 2021-01-12T06:59:52Z
day: '27'
ddc:
- '570'
department:
- _id: ToBo
doi: 10.1371/journal.pgen.1003580
file:
- access_level: open_access
checksum: 7a4736dd80496d29ff6908b6f2329b4e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:51Z
date_updated: 2020-07-14T12:45:48Z
file_id: '4713'
file_name: IST-2016-412-v1+1_journal.pgen.1003580.pdf
file_size: 474655
relation: main_file
file_date_updated: 2020-07-14T12:45:48Z
has_accepted_license: '1'
intvolume: ' 9'
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: PLoS Genetics
publication_status: published
publisher: Public Library of Science
publist_id: '4075'
pubrep_id: '412'
quality_controlled: '1'
scopus_import: 1
status: public
title: Environmental dependence of genetic constraint
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2013'
...