Jie Deng
@jie-eco.bsky.social
Theoretical ecologist @ox.ac.uk
sites.google.com/view/dengjie
sites.google.com/view/dengjie
Pinned
Jie Deng
@jie-eco.bsky.social
· Nov 15
I'm giving this a try to provide a quick and clear summary of our recent work on ecological development in
@currentbiology.bsky.social, hoping to share some useful insights without taking up too much of your time. 😁 #Ecology #Biodiversity
@currentbiology.bsky.social, hoping to share some useful insights without taking up too much of your time. 😁 #Ecology #Biodiversity
Reposted by Jie Deng
#NewResearch
Strain displacement in microbiomes via ecological competition
@erikbakkeren.bsky.social
#microsky
www.nature.com/articles/s41...
Strain displacement in microbiomes via ecological competition
@erikbakkeren.bsky.social
#microsky
www.nature.com/articles/s41...
Strain displacement in microbiomes via ecological competition - Nature Microbiology
Mathematical modelling and experimental tests reveal principles that govern displacement of a resident strain by an invader in microbial communities.
www.nature.com
November 7, 2025 at 11:09 AM
#NewResearch
Strain displacement in microbiomes via ecological competition
@erikbakkeren.bsky.social
#microsky
www.nature.com/articles/s41...
Strain displacement in microbiomes via ecological competition
@erikbakkeren.bsky.social
#microsky
www.nature.com/articles/s41...
Reposted by Jie Deng
Paradoxical role of new endosymbiotic associations: they facilitate the emergence of new partnerships, but inhibit deeper integration between hosts and guests (by favoring uncoordinated reproduction over synchronized ones). That is, easy come, easy go. #Endosymbiosis doi.org/10.1101/2025...
October 29, 2025 at 3:41 PM
Paradoxical role of new endosymbiotic associations: they facilitate the emergence of new partnerships, but inhibit deeper integration between hosts and guests (by favoring uncoordinated reproduction over synchronized ones). That is, easy come, easy go. #Endosymbiosis doi.org/10.1101/2025...
Reposted by Jie Deng
NYC and adjacent friends: I'm thrilled and terrified to be giving a public lecture in Manhattan at 6pm on Wednesday, 19 November. If you feel like coming into the city* for the evening, I'd love to see you there!
*Yes, NYC = "the city" for Jersey girls.
www.simonsfoundation.org/event/trade-...
*Yes, NYC = "the city" for Jersey girls.
www.simonsfoundation.org/event/trade-...
Trade, Borrow, or Steal: How Acquired Metabolism Drives Evolution
Trade, Borrow, or Steal: How Acquired Metabolism Drives Evolution on Simons Foundation
www.simonsfoundation.org
November 3, 2025 at 1:34 AM
NYC and adjacent friends: I'm thrilled and terrified to be giving a public lecture in Manhattan at 6pm on Wednesday, 19 November. If you feel like coming into the city* for the evening, I'd love to see you there!
*Yes, NYC = "the city" for Jersey girls.
www.simonsfoundation.org/event/trade-...
*Yes, NYC = "the city" for Jersey girls.
www.simonsfoundation.org/event/trade-...
Research Assistant or Associate opportunity at Imperial College London: Conduct temperature-resolved microbial experiments to understand how microbes adapt and thrive across thermal environments 🌡️🧫
www.imperial.ac.uk/jobs/search-...
www.imperial.ac.uk/jobs/search-...
Description
Please note that job descriptions are not exhaustive, and you may be asked to take on additional duties that align with the key responsibilities ment...
www.imperial.ac.uk
October 11, 2025 at 1:42 PM
Research Assistant or Associate opportunity at Imperial College London: Conduct temperature-resolved microbial experiments to understand how microbes adapt and thrive across thermal environments 🌡️🧫
www.imperial.ac.uk/jobs/search-...
www.imperial.ac.uk/jobs/search-...
Reposted by Jie Deng
Are you a postdoc interested in the mechanisms of disease?
Do you have a great record and an exciting vision?
Come and start your own lab @dunnschool.bsky.social by applying for sponsorship for early career fellowships.
Deadline 30th September...pass it on!
www.path.ox.ac.uk/work-with-us...
Do you have a great record and an exciting vision?
Come and start your own lab @dunnschool.bsky.social by applying for sponsorship for early career fellowships.
Deadline 30th September...pass it on!
www.path.ox.ac.uk/work-with-us...
Group Leader Career Development Fellowships - Dunn School
Are you an early career researcher interested in the cell or molecular mechanisms underlying disease? Do you have an outstanding record and an innovative research plan?
www.path.ox.ac.uk
September 1, 2025 at 2:39 PM
Are you a postdoc interested in the mechanisms of disease?
Do you have a great record and an exciting vision?
Come and start your own lab @dunnschool.bsky.social by applying for sponsorship for early career fellowships.
Deadline 30th September...pass it on!
www.path.ox.ac.uk/work-with-us...
Do you have a great record and an exciting vision?
Come and start your own lab @dunnschool.bsky.social by applying for sponsorship for early career fellowships.
Deadline 30th September...pass it on!
www.path.ox.ac.uk/work-with-us...
Reposted by Jie Deng
New study by @mucosalimmunology.bsky.social (Dunn School and @ethzurich.bsky.social) with Médéric Diard (@biozentrum.unibas.ch) reveals how combining vaccines with friendly bacteria can boost vaccination efficacy and potentially reduce reliance on antibiotics
www.path.ox.ac.uk/news-article...
www.path.ox.ac.uk/news-article...
Boosting vaccines with harmless bacteria to fight intestinal pathogens - Dunn School
Published in Science, a ground-breaking study by the Slack group reveals how combining vaccines with friendly bacteria can boost vaccination efficacy and potentially reduce reliance on antibiotics.
www.path.ox.ac.uk
April 4, 2025 at 10:30 AM
New study by @mucosalimmunology.bsky.social (Dunn School and @ethzurich.bsky.social) with Médéric Diard (@biozentrum.unibas.ch) reveals how combining vaccines with friendly bacteria can boost vaccination efficacy and potentially reduce reliance on antibiotics
www.path.ox.ac.uk/news-article...
www.path.ox.ac.uk/news-article...
Reposted by Jie Deng
Does your lab perform killing assays?
TL;DR: we’ve identified a problem that can bias the outcome of killing assays, making antagonism look stronger than it really is.
Adding a simple extra step can mitigate this bias!

Out now at #MicrobioJ www.microbiologyresearch.org/content/jour...
1/n
TL;DR: we’ve identified a problem that can bias the outcome of killing assays, making antagonism look stronger than it really is.
Adding a simple extra step can mitigate this bias!

Out now at #MicrobioJ www.microbiologyresearch.org/content/jour...
1/n
Type VI secretion system activity at lethal antibiotic concentrations leads to overestimation of weapon potency
Competition assays are a mainstay of modern microbiology, offering a simple and cost-effective means to quantify microbe–microbe interactions in vitro. Here, we demonstrate a key weakness of this meth...
www.microbiologyresearch.org
August 31, 2025 at 9:30 PM
Does your lab perform killing assays?
TL;DR: we’ve identified a problem that can bias the outcome of killing assays, making antagonism look stronger than it really is.
Adding a simple extra step can mitigate this bias!

Out now at #MicrobioJ www.microbiologyresearch.org/content/jour...
1/n
TL;DR: we’ve identified a problem that can bias the outcome of killing assays, making antagonism look stronger than it really is.
Adding a simple extra step can mitigate this bias!

Out now at #MicrobioJ www.microbiologyresearch.org/content/jour...
1/n
Reposted by Jie Deng
#Bacteria use weapons to outcompete rivals, but what happens if they're transferred? @prokaryota.bsky.social @jdpal.bsky.social &co show that HGT of toxin #plasmids is rare but recipients can thrive under relaxed nutrient competition, reshaping bacterial warfare @plosbiology.org 🧪 plos.io/43vC3X7
May 22, 2025 at 9:00 AM
#Bacteria use weapons to outcompete rivals, but what happens if they're transferred? @prokaryota.bsky.social @jdpal.bsky.social &co show that HGT of toxin #plasmids is rare but recipients can thrive under relaxed nutrient competition, reshaping bacterial warfare @plosbiology.org 🧪 plos.io/43vC3X7
Reposted by Jie Deng
Please read about how we think microbial metabolism might help us understand microbiomes a bit better!
Also, please appreciate the mountain goat in Fig 1 ⛰️🐐 and that it also represents my joy for trail running and the mountains 😁
Also, please appreciate the mountain goat in Fig 1 ⛰️🐐 and that it also represents my joy for trail running and the mountains 😁
Metabolic ecology of microbiomes: Nutrient competition, host benefits, and community engineering
Review by Erik Bakkeren, Vit Piskovsky, and Kevin R. Foster
www.cell.com/cell-host-mi...
Review by Erik Bakkeren, Vit Piskovsky, and Kevin R. Foster
www.cell.com/cell-host-mi...
June 11, 2025 at 5:08 PM
Please read about how we think microbial metabolism might help us understand microbiomes a bit better!
Also, please appreciate the mountain goat in Fig 1 ⛰️🐐 and that it also represents my joy for trail running and the mountains 😁
Also, please appreciate the mountain goat in Fig 1 ⛰️🐐 and that it also represents my joy for trail running and the mountains 😁
Reposted by Jie Deng
Excited to see our latest work published on GEB! We comprehensively compared various environmental predictability measures, their impact on statistical analyses and their global patterns 🤩
what is environmental variability and how can you measure it? onlinelibrary.wiley.com/doi/10.1111/... @mingpapilio.bsky.social
Environmental Predictability in Phylogenetic Comparative Analysis: How to Measure It and Does It Matter?
Aim Abiotic environmental conditions shape ecological and evolutionary processes, yet quantifying their influence on organisms remains challenging due to variation among metrics and their intercorre...
onlinelibrary.wiley.com
August 16, 2025 at 8:10 PM
Excited to see our latest work published on GEB! We comprehensively compared various environmental predictability measures, their impact on statistical analyses and their global patterns 🤩
Research Assistant opportunity in the Coyte Lab (University of Manchester): Lead analyses of large-scale, longitudinal datasets (already collected) exploring the dynamics of the mammalian immune system and gut microbiome 🦠
www.jobs.manchester.ac.uk/Job/JobDetai...
www.jobs.manchester.ac.uk/Job/JobDetai...
Research Associate in Microbiome Dynamics:Oxford Road
The Coyte Lab group within the Division of Evolution, Infection and Genomics wishes to appoint a Research Associate to an exciting project exploring the interplay between the mammalian immune system and gut microbiome, funded by an 8-year Wellcome CDA in collaboration with Prof. Matthew Hepworth.
www.jobs.manchester.ac.uk
August 28, 2025 at 12:06 PM
Research Assistant opportunity in the Coyte Lab (University of Manchester): Lead analyses of large-scale, longitudinal datasets (already collected) exploring the dynamics of the mammalian immune system and gut microbiome 🦠
www.jobs.manchester.ac.uk/Job/JobDetai...
www.jobs.manchester.ac.uk/Job/JobDetai...
PDRA opportunity in the Coyte Lab at Manchester: modelling carbon-fixing microbial communities in Icelandic hot springs 🌋, with chances for field trips to some very beautiful places! www.jobs.manchester.ac.uk/Job/JobDetai...
Research Associate in Microbiome Ecology:Oxford Road
www.jobs.manchester.ac.uk
August 12, 2025 at 3:49 PM
PDRA opportunity in the Coyte Lab at Manchester: modelling carbon-fixing microbial communities in Icelandic hot springs 🌋, with chances for field trips to some very beautiful places! www.jobs.manchester.ac.uk/Job/JobDetai...
Reposted by Jie Deng
Our article on the challenges and opportunities in studying host-microbe symbioses is now published in Cell Host & Microbe! @cp-cellhostmicrobe.bsky.social
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Theory of host-microbe symbioses: Challenges and opportunities
Growing insight into microbial symbioses highlights the need to model these systems mathematically. We discuss three areas requiring theoretical advan…
www.sciencedirect.com
July 9, 2025 at 7:00 PM
Our article on the challenges and opportunities in studying host-microbe symbioses is now published in Cell Host & Microbe! @cp-cellhostmicrobe.bsky.social
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Reposted by Jie Deng
We are on the lookout for postdocs for two different projects at the intersection of ecology, evolution, and the human microbiome.
See thread for more information and reach out!
See thread for more information and reach out!
July 22, 2025 at 7:34 PM
We are on the lookout for postdocs for two different projects at the intersection of ecology, evolution, and the human microbiome.
See thread for more information and reach out!
See thread for more information and reach out!
Reposted by Jie Deng
This project is in collaboration with @jacrickets.bsky.social and Shawn McGlynn!
July 23, 2025 at 6:41 PM
This project is in collaboration with @jacrickets.bsky.social and Shawn McGlynn!
Reposted by Jie Deng
Happy to share a new preprint! W/ @zachgold.bsky.social, Haylee Oyler, Jonathan Levine and @nathanjbkraft.bsky.social. We use a spatially explicit experimental design to ask:
do higher-order interactions structure the dynamics of annual plant communities?
Link: www.biorxiv.org/content/10.1...
🧵
do higher-order interactions structure the dynamics of annual plant communities?
Link: www.biorxiv.org/content/10.1...
🧵
July 21, 2025 at 1:51 PM
Happy to share a new preprint! W/ @zachgold.bsky.social, Haylee Oyler, Jonathan Levine and @nathanjbkraft.bsky.social. We use a spatially explicit experimental design to ask:
do higher-order interactions structure the dynamics of annual plant communities?
Link: www.biorxiv.org/content/10.1...
🧵
do higher-order interactions structure the dynamics of annual plant communities?
Link: www.biorxiv.org/content/10.1...
🧵
Reposted by Jie Deng
Last year, I joined a brilliant group of researchers for a 3-week deep dive into host–microbe systems. Each week explored a different theme, led by inspiring lecturers.
I’m excited to share that videos of their talks — along with presentations by several team members — are now on YouTube:
I’m excited to share that videos of their talks — along with presentations by several team members — are now on YouTube:
July 18, 2025 at 5:41 PM
Last year, I joined a brilliant group of researchers for a 3-week deep dive into host–microbe systems. Each week explored a different theme, led by inspiring lecturers.
I’m excited to share that videos of their talks — along with presentations by several team members — are now on YouTube:
I’m excited to share that videos of their talks — along with presentations by several team members — are now on YouTube:
Reposted by Jie Deng
Host Competitive Asymmetries Accelerate Viral Evolution in a Microbe–Virus Coevolutionary System - Liaghat - 2025 - Ecology Letters - Wiley Online Library onlinelibrary.wiley.com/doi/10.1111/...
onlinelibrary.wiley.com
June 20, 2025 at 3:29 PM
Host Competitive Asymmetries Accelerate Viral Evolution in a Microbe–Virus Coevolutionary System - Liaghat - 2025 - Ecology Letters - Wiley Online Library onlinelibrary.wiley.com/doi/10.1111/...
Reposted by Jie Deng
New paper w/ Jonathan Levine and @exp-evoeco.bsky.social! We induced plastic responses in annual plants through early-life competition. These responses tended to make subsequent species interactions stronger and coexistence less likely.
Link: esajournals.onlinelibrary.wiley.com/doi/10.1002/...
Link: esajournals.onlinelibrary.wiley.com/doi/10.1002/...
May 12, 2025 at 5:26 PM
New paper w/ Jonathan Levine and @exp-evoeco.bsky.social! We induced plastic responses in annual plants through early-life competition. These responses tended to make subsequent species interactions stronger and coexistence less likely.
Link: esajournals.onlinelibrary.wiley.com/doi/10.1002/...
Link: esajournals.onlinelibrary.wiley.com/doi/10.1002/...
Reposted by Jie Deng
**NEW DATABASE** - and it's a big one: BioTIME 2.0 is out!
I'll guide you through why this database is a game changer for anyone interested in species on the move
--> the3dlab.org/2025/05/21/b...
The paper --> doi.org/10.1111/geb....
I'll guide you through why this database is a game changer for anyone interested in species on the move
--> the3dlab.org/2025/05/21/b...
The paper --> doi.org/10.1111/geb....
BioTime 2.0
If we want to understand how biodiversity is shifting in this rapidly changing climate, we need two critical ingredients: microclimate time series and biodiversity time series. (And yes, let’s not …
the3dlab.org
May 21, 2025 at 7:58 AM
**NEW DATABASE** - and it's a big one: BioTIME 2.0 is out!
I'll guide you through why this database is a game changer for anyone interested in species on the move
--> the3dlab.org/2025/05/21/b...
The paper --> doi.org/10.1111/geb....
I'll guide you through why this database is a game changer for anyone interested in species on the move
--> the3dlab.org/2025/05/21/b...
The paper --> doi.org/10.1111/geb....
Reposted by Jie Deng
Super honoured to have been recognised by the ENDS Power List 2025 for my work on Biodiversity Net Gain and invertebrates! 🪲🌱
www.endsreport.com/article/1918...
www.endsreport.com/article/1918...
Power List 2025: The UK’s 100 most impactful environmental professionals
www.endsreport.com
May 19, 2025 at 12:10 PM
Super honoured to have been recognised by the ENDS Power List 2025 for my work on Biodiversity Net Gain and invertebrates! 🪲🌱
www.endsreport.com/article/1918...
www.endsreport.com/article/1918...
Reposted by Jie Deng
We are pleased to announce the 90 outstanding researchers from across the world who have been elected to the Fellowship of the Royal Society this year. The group includes trailblazers from AI and electron microscopy to global health and neuroscience. #RSFellows royalsociety.org/news/2025/05...
Exceptional scientists elected as Fellows of the Royal Society | Royal Society
Over 90 outstanding researchers from across the world have this year been elected to the Fellowship of the Royal Society, the UK’s national academy of sciences.
royalsociety.org
May 20, 2025 at 9:31 AM
We are pleased to announce the 90 outstanding researchers from across the world who have been elected to the Fellowship of the Royal Society this year. The group includes trailblazers from AI and electron microscopy to global health and neuroscience. #RSFellows royalsociety.org/news/2025/05...
Reposted by Jie Deng
Delighted to announce that Prof. Kevin Foster has been elected Fellow of @royalsociety.org!
This honour recognises the unique way he combines maths, ecology, evolution and microbiology to study microbial communities
Many congratulations Kevin!
Find out more: www.path.ox.ac.uk/news-article...
This honour recognises the unique way he combines maths, ecology, evolution and microbiology to study microbial communities
Many congratulations Kevin!
Find out more: www.path.ox.ac.uk/news-article...
Kevin Foster elected Fellow of the Royal Society - Dunn School
Many congratulations to Kevin for this prestigious honour, recognising his contribution to integrate ecological and evolutionary principles into microbiology to understand the human microbiome and oth...
www.path.ox.ac.uk
May 20, 2025 at 9:13 AM
Delighted to announce that Prof. Kevin Foster has been elected Fellow of @royalsociety.org!
This honour recognises the unique way he combines maths, ecology, evolution and microbiology to study microbial communities
Many congratulations Kevin!
Find out more: www.path.ox.ac.uk/news-article...
This honour recognises the unique way he combines maths, ecology, evolution and microbiology to study microbial communities
Many congratulations Kevin!
Find out more: www.path.ox.ac.uk/news-article...
PhD opportunity at Manchester: using math modelling + bioreactors to study how temperate and lytic phages interact. Open to international applicants: www.findaphd.com/phds/project...
(EPSRC DTP) How do the interactions between temperate and lytic phages shape microbial communities? at The University of Manchester on FindAPhD.com
PhD Project - (EPSRC DTP) How do the interactions between temperate and lytic phages shape microbial communities? at The University of Manchester, listed on FindAPhD.com
www.findaphd.com
May 20, 2025 at 10:05 AM
PhD opportunity at Manchester: using math modelling + bioreactors to study how temperate and lytic phages interact. Open to international applicants: www.findaphd.com/phds/project...
Reposted by Jie Deng
We are recruiting @ox.ac.uk @dunnschool.bsky.social for a joint project between Kevin Foster's group and mine! Cluster hire of two postdocs interested in:
1) Mucosal immunology and oral vaccine development
my.corehr.com/pls/uoxrecru...
2) Microbiology
my.corehr.com/pls/uoxrecru...
Please share!
1) Mucosal immunology and oral vaccine development
my.corehr.com/pls/uoxrecru...
2) Microbiology
my.corehr.com/pls/uoxrecru...
Please share!
'
my.corehr.com
February 22, 2025 at 8:07 PM
We are recruiting @ox.ac.uk @dunnschool.bsky.social for a joint project between Kevin Foster's group and mine! Cluster hire of two postdocs interested in:
1) Mucosal immunology and oral vaccine development
my.corehr.com/pls/uoxrecru...
2) Microbiology
my.corehr.com/pls/uoxrecru...
Please share!
1) Mucosal immunology and oral vaccine development
my.corehr.com/pls/uoxrecru...
2) Microbiology
my.corehr.com/pls/uoxrecru...
Please share!