Aidan Foo, PhD
@aidanfoo.bsky.social
Microbial genomics and mosquito microbiomes | Research Tech @ The Liverpool School of Tropical Medicine
GitHub: https://github.com/aidanfoo96
LinkedIN: https://www.linkedin.com/in/aidan-foo
GitHub: https://github.com/aidanfoo96
LinkedIN: https://www.linkedin.com/in/aidan-foo
Reposted by Aidan Foo, PhD
And it’s been a while since I dipped my toe into the questions of what ‘species’ might mean for bacteria, and how they relate to ecology. But still interests me! genomebiology.biomedcentral.com/articles/10....
Relating ecological diversity to genetic discontinuity across bacterial species - Genome Biology
Background Genetic discontinuity represents abrupt breaks in genomic identity among species. Advances in genome sequencing have enhanced our ability to track and characterize genetic discontinuity in ...
genomebiology.biomedcentral.com
January 13, 2025 at 3:43 PM
And it’s been a while since I dipped my toe into the questions of what ‘species’ might mean for bacteria, and how they relate to ecology. But still interests me! genomebiology.biomedcentral.com/articles/10....
Reposted by Aidan Foo, PhD
Emerging models to study competitive interactions within bacterial communities www.cell.com/trends/micro... #jcampubs
Emerging models to study competitive interactions within bacterial communities
Within both abiotic and host environments, bacteria typically exist as diverse, multispecies
communities and have crucial roles in human health, agriculture, and industry. In
these communities, bacter...
www.cell.com
January 13, 2025 at 5:32 PM
Emerging models to study competitive interactions within bacterial communities www.cell.com/trends/micro... #jcampubs
Reposted by Aidan Foo, PhD
Thrilled to announce that our work (w. with fantastic @neher.io and Liam Shaw) has been published on Molecular Biology and Evolution! 🎉
academic.oup.com/mbe/advance-...
Are you curious about how fast the genome of E.coli evolves structurally (gains, rearrangements...) ? 🧬
A summary thread [1/N]🧵
academic.oup.com/mbe/advance-...
Are you curious about how fast the genome of E.coli evolves structurally (gains, rearrangements...) ? 🧬
A summary thread [1/N]🧵
Quantifying the evolutionary dynamics of structure and content in closely-related E. coli genomes
Abstract. Bacterial genomes primarily diversify via gain, loss, and rearrangement of genetic material in their flexible accessory genome. Yet the dynamics
academic.oup.com
January 6, 2025 at 5:12 PM
Thrilled to announce that our work (w. with fantastic @neher.io and Liam Shaw) has been published on Molecular Biology and Evolution! 🎉
academic.oup.com/mbe/advance-...
Are you curious about how fast the genome of E.coli evolves structurally (gains, rearrangements...) ? 🧬
A summary thread [1/N]🧵
academic.oup.com/mbe/advance-...
Are you curious about how fast the genome of E.coli evolves structurally (gains, rearrangements...) ? 🧬
A summary thread [1/N]🧵
Reposted by Aidan Foo, PhD
High-dose VE303, a bacterial consortium, reduced recurrent C. difficile infection risk by over 80% in phase 2 trials. Promising alternative to fecal transplants! #Microbiome PMID:39747680, Nat Med 2025, @NatureMedicine
Multi-omic profiling a defined bacterial consortium for treatment of recurrent Clostridioides difficile infection
Results of multi-omic profiling of the microbiome and host immunity of individuals treated with VE303 to prevent recurrent Clostridioides difficile infection in the context of a phase 2 trial show robust...
buff.ly
January 4, 2025 at 7:37 PM
High-dose VE303, a bacterial consortium, reduced recurrent C. difficile infection risk by over 80% in phase 2 trials. Promising alternative to fecal transplants! #Microbiome PMID:39747680, Nat Med 2025, @NatureMedicine
Reposted by Aidan Foo, PhD
New year, new assemblies!
I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: github.com/rrwick/Autoc...
(1/5)
I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: github.com/rrwick/Autoc...
(1/5)
Home
A tool for generating consensus long-read assemblies for bacterial genomes - rrwick/Autocycler
github.com
December 31, 2024 at 11:43 PM
New year, new assemblies!
I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: github.com/rrwick/Autoc...
(1/5)
I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: github.com/rrwick/Autoc...
(1/5)
Reposted by Aidan Foo, PhD
Phylogenetic and functional diversity among Drosophila-associated metagenome-assembled genomes http://biorxiv.org/cgi/content/short/2024.12.19.629488v1
December 24, 2024 at 8:54 AM
Phylogenetic and functional diversity among Drosophila-associated metagenome-assembled genomes http://biorxiv.org/cgi/content/short/2024.12.19.629488v1
Reposted by Aidan Foo, PhD
Published just in time for the holidays! I learned so much while writing about the past, present, and future of E. faecalis research with Gary. Check it out! 🦠🧫🧪🔬
journals.asm.org/doi/10.1128/...
journals.asm.org/doi/10.1128/...
Insights into ecology, pathogenesis, and biofilm formation of Enterococcus faecalis from functional genomics | Microbiology and Molecular Biology Reviews
SUMMARYEnterococcus faecalis is a significant resident of the gastrointestinal tract of most animals, including humans. Although generally non-pathogenic in healthy hosts, this microbe is adept at the exploitation of compromises in host immune functions, ...
journals.asm.org
December 23, 2024 at 6:07 PM
Published just in time for the holidays! I learned so much while writing about the past, present, and future of E. faecalis research with Gary. Check it out! 🦠🧫🧪🔬
journals.asm.org/doi/10.1128/...
journals.asm.org/doi/10.1128/...
Reposted by Aidan Foo, PhD
End of year science thread: a few memorable papers that came out this year. 1) Beavan ft. @blackpassiflora.bsky.social and @jomcinerney.bsky.social found ML models predicted co-occurrence of many genes in microbial pangenomes.
🧪 1/7
pnas.org/doi/10.1073/...
🧪 1/7
pnas.org/doi/10.1073/...
Contingency, repeatability, and predictability in the evolution of a prokaryotic pangenome | PNAS
Pangenomes exhibit remarkable variability in many prokaryotic species, much of which
is maintained through the processes of horizontal gene transfe...
pnas.org
December 20, 2024 at 7:16 PM
End of year science thread: a few memorable papers that came out this year. 1) Beavan ft. @blackpassiflora.bsky.social and @jomcinerney.bsky.social found ML models predicted co-occurrence of many genes in microbial pangenomes.
🧪 1/7
pnas.org/doi/10.1073/...
🧪 1/7
pnas.org/doi/10.1073/...
Reposted by Aidan Foo, PhD
relevant to a paper I just reviewed (and cited this paper bmcbiol.biomedcentral.com/articles/10....). Ppl seem resistant to this lesson...
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses - BMC Biology
Background The study of microbial communities has been revolutionised in recent years by the widespread adoption of culture independent analytical techniques such as 16S rRNA gene sequencing and metag...
bmcbiol.biomedcentral.com
December 20, 2024 at 7:18 PM
relevant to a paper I just reviewed (and cited this paper bmcbiol.biomedcentral.com/articles/10....). Ppl seem resistant to this lesson...
Reposted by Aidan Foo, PhD
A collaborative perspective on eco-evolutionary dynamics of antimicrobial resistance in the context of One Health.
An eco-evolutionary perspective on antimicrobial resistance in the context of One Health
Health sciences; Biological sciences; Microbiology; Evolutionary biology
www.cell.com
December 18, 2024 at 12:40 PM
A collaborative perspective on eco-evolutionary dynamics of antimicrobial resistance in the context of One Health.
Reposted by Aidan Foo, PhD
Lovely week to finish the year for the @mossi-lab.bsky.social lab. @aidanfoo.bsky.social doing fantastic work at his viva and Ana Pitol securing a lecturer position @lstmnews.bsky.social!
Huge congratulations to Dr @aidanfoo.bsky.social who passed his viva yesterday!
@mosquitomicrobe.bsky.social
@gemma-langridge.bsky.social
@mosquitomicrobe.bsky.social
@gemma-langridge.bsky.social
December 17, 2024 at 9:24 PM
Lovely week to finish the year for the @mossi-lab.bsky.social lab. @aidanfoo.bsky.social doing fantastic work at his viva and Ana Pitol securing a lecturer position @lstmnews.bsky.social!
Reposted by Aidan Foo, PhD
Huge congratulations to Dr @aidanfoo.bsky.social who passed his viva yesterday!
@mosquitomicrobe.bsky.social
@gemma-langridge.bsky.social
@mosquitomicrobe.bsky.social
@gemma-langridge.bsky.social
December 17, 2024 at 10:25 AM
Huge congratulations to Dr @aidanfoo.bsky.social who passed his viva yesterday!
@mosquitomicrobe.bsky.social
@gemma-langridge.bsky.social
@mosquitomicrobe.bsky.social
@gemma-langridge.bsky.social
Reposted by Aidan Foo, PhD
Thanks so much to the @unistrathclyde.bsky.social comms team to give us an extra shout-out on our recent #mosquito #microbiome bacterial isolate analyses! Extra gold star to @aidanfoo.bsky.social's outstanding coding & DataViz skills 🌟 #MicroSky #MicrobiomeSky 🧬💻 www.strath.ac.uk/whystrathcly...
Novel community resource could create new ways to stop the spread of diseases carried by mosquitoes | University of Strathclyde
www.strath.ac.uk
December 12, 2024 at 8:46 AM
Thanks so much to the @unistrathclyde.bsky.social comms team to give us an extra shout-out on our recent #mosquito #microbiome bacterial isolate analyses! Extra gold star to @aidanfoo.bsky.social's outstanding coding & DataViz skills 🌟 #MicroSky #MicrobiomeSky 🧬💻 www.strath.ac.uk/whystrathcly...
Reposted by Aidan Foo, PhD
If an #H5N1 pandemic starts tomorrow or in three months, there will be little mystery as to how it happened. The conditions are all there. They have been for a while.
So in some ways the more interesting question to me at the moment is: Why aren’t we in a pandemic yet?
Story here, 🧵 to come:
🧪#IDSky
So in some ways the more interesting question to me at the moment is: Why aren’t we in a pandemic yet?
Story here, 🧵 to come:
🧪#IDSky
Why hasn’t the bird flu pandemic started?
Some scientists examining mutations found in H5N1 viruses fear major outbreak is imminent but others says pathogen remains unpredictable
www.science.org
December 6, 2024 at 12:54 PM
If an #H5N1 pandemic starts tomorrow or in three months, there will be little mystery as to how it happened. The conditions are all there. They have been for a while.
So in some ways the more interesting question to me at the moment is: Why aren’t we in a pandemic yet?
Story here, 🧵 to come:
🧪#IDSky
So in some ways the more interesting question to me at the moment is: Why aren’t we in a pandemic yet?
Story here, 🧵 to come:
🧪#IDSky
Reposted by Aidan Foo, PhD
Bactopia now supports AllTheBacteria assemblies!
If you are planning secondary analyses, this feature allows you to seamlessly use Bactopia.
To demonstrate this, here's a blog post using Bactopia to analyze 5400 L. pneumophila assemblies
bactopia.github.io/latest/blog/...
If you are planning secondary analyses, this feature allows you to seamlessly use Bactopia.
To demonstrate this, here's a blog post using Bactopia to analyze 5400 L. pneumophila assemblies
bactopia.github.io/latest/blog/...
March 26, 2024 at 12:59 AM
Bactopia now supports AllTheBacteria assemblies!
If you are planning secondary analyses, this feature allows you to seamlessly use Bactopia.
To demonstrate this, here's a blog post using Bactopia to analyze 5400 L. pneumophila assemblies
bactopia.github.io/latest/blog/...
If you are planning secondary analyses, this feature allows you to seamlessly use Bactopia.
To demonstrate this, here's a blog post using Bactopia to analyze 5400 L. pneumophila assemblies
bactopia.github.io/latest/blog/...
Reposted by Aidan Foo, PhD
on 𝕏: @PLOSBiology
The #phylogenetic tree has been a core conceptual tool for #EvolutionaryBiology for nearly 200 years. @RoliRoberts explores the role of the tree as a metaphor, discussing two new #PLOSBiology Essays that look to the future plos.io/3VjDSU8
The #phylogenetic tree has been a core conceptual tool for #EvolutionaryBiology for nearly 200 years. @RoliRoberts explores the role of the tree as a metaphor, discussing two new #PLOSBiology Essays that look to the future plos.io/3VjDSU8
Trees as a metaphor to understand relationships in biology
The phylogenetic tree has been a core conceptual tool for evolutionary biology for nearly 200 years. This editorial explores the role of the tree as a metaphor, discussing two new PLOS Biology Essays ...
plos.io
May 29, 2024 at 7:58 PM
on 𝕏: @PLOSBiology
The #phylogenetic tree has been a core conceptual tool for #EvolutionaryBiology for nearly 200 years. @RoliRoberts explores the role of the tree as a metaphor, discussing two new #PLOSBiology Essays that look to the future plos.io/3VjDSU8
The #phylogenetic tree has been a core conceptual tool for #EvolutionaryBiology for nearly 200 years. @RoliRoberts explores the role of the tree as a metaphor, discussing two new #PLOSBiology Essays that look to the future plos.io/3VjDSU8
Reposted by Aidan Foo, PhD
A new and very important study on the global evolutionary patterns of Yersinia pestis and its spread into Africa
#MicroSky, #IDSky
www.biorxiv.org/content/10.1...
#MicroSky, #IDSky
www.biorxiv.org/content/10.1...
November 29, 2024 at 6:46 AM
A new and very important study on the global evolutionary patterns of Yersinia pestis and its spread into Africa
#MicroSky, #IDSky
www.biorxiv.org/content/10.1...
#MicroSky, #IDSky
www.biorxiv.org/content/10.1...
Reposted by Aidan Foo, PhD
Bifidobacteriaceae diversity in the human microbiome from a large-scale genome-wide analysis https://pubmed.ncbi.nlm.nih.gov/39602306/
November 29, 2024 at 8:20 AM
Bifidobacteriaceae diversity in the human microbiome from a large-scale genome-wide analysis https://pubmed.ncbi.nlm.nih.gov/39602306/
Reposted by Aidan Foo, PhD
Lots of MosSI Lab representation at the LSTM 125th Scientific Symposium this week!
@mosquitomicrobe.bsky.social spoke about our Anopheles Wolbachia work.
@mosquitomicrobe.bsky.social spoke about our Anopheles Wolbachia work.
November 27, 2024 at 3:54 PM
Lots of MosSI Lab representation at the LSTM 125th Scientific Symposium this week!
@mosquitomicrobe.bsky.social spoke about our Anopheles Wolbachia work.
@mosquitomicrobe.bsky.social spoke about our Anopheles Wolbachia work.
Reposted by Aidan Foo, PhD
Hot off the press - some light reading on Shigella sonnei! 🧪🧫🧬
With @ksbakes.bsky.social @yekwah.bsky.social @sydneylmiles.bsky.social @sergemostowylab.bsky.social @lshtmamrcentre.bsky.social and a bunch of others not yet on bluesky rdcu.be/d1EAF
With @ksbakes.bsky.social @yekwah.bsky.social @sydneylmiles.bsky.social @sergemostowylab.bsky.social @lshtmamrcentre.bsky.social and a bunch of others not yet on bluesky rdcu.be/d1EAF
Shigella sonnei: epidemiology, evolution, pathogenesis, resistance and host interactions
Nature Reviews Microbiology - In this Review, Scott et al. review our current knowledge of Shigella sonnei, highlighting recent insights into this globally disseminated antimicrobial-resistant...
rdcu.be
November 27, 2024 at 1:33 PM
Hot off the press - some light reading on Shigella sonnei! 🧪🧫🧬
With @ksbakes.bsky.social @yekwah.bsky.social @sydneylmiles.bsky.social @sergemostowylab.bsky.social @lshtmamrcentre.bsky.social and a bunch of others not yet on bluesky rdcu.be/d1EAF
With @ksbakes.bsky.social @yekwah.bsky.social @sydneylmiles.bsky.social @sergemostowylab.bsky.social @lshtmamrcentre.bsky.social and a bunch of others not yet on bluesky rdcu.be/d1EAF
Reposted by Aidan Foo, PhD
I often get asked what is the best place to start to learn more about the human microbiome for those new to the field. I always default to this excellent collection that was put together by @npariente.bsky.social and Ashley York: www.nature.com/immersive/d4.... Any other good recommendations?
Milestones in Human Microbiota Research
www.nature.com
November 27, 2024 at 9:11 AM
I often get asked what is the best place to start to learn more about the human microbiome for those new to the field. I always default to this excellent collection that was put together by @npariente.bsky.social and Ashley York: www.nature.com/immersive/d4.... Any other good recommendations?
Reposted by Aidan Foo, PhD
The @mossi-lab.bsky.social has several PhD projects on offer at LSTM. Flavours include Wolbachia in Anopheles, microbiome mosquito interactions, Wolbachia-microbiome interactions, & antiviral in mosquitoes.
Students should apply to the LSTM PhD program - Applications close on the 4th of December!
Students should apply to the LSTM PhD program - Applications close on the 4th of December!
MRC DTP/CASE: How to apply
Stage 1During stage one we will ask you to submit a form consisting of:Title, name, contact details, nationality and fee statusSelection of your preferred project choiceMotivation for applying to the
www.lstmed.ac.uk
November 24, 2024 at 7:38 PM
The @mossi-lab.bsky.social has several PhD projects on offer at LSTM. Flavours include Wolbachia in Anopheles, microbiome mosquito interactions, Wolbachia-microbiome interactions, & antiviral in mosquitoes.
Students should apply to the LSTM PhD program - Applications close on the 4th of December!
Students should apply to the LSTM PhD program - Applications close on the 4th of December!
Reposted by Aidan Foo, PhD
Check out the new work from the MosSI lab in collaboration with @aidanfoo.bsky.social @laurabrettell.bsky.social @evaheinz7.bsky.social and heaps of others.
MosAIC: An annotated collection of mosquito-associated bacteria with high-quality genome assemblies
journals.plos.org/plosbiology/...
MosAIC: An annotated collection of mosquito-associated bacteria with high-quality genome assemblies
journals.plos.org/plosbiology/...
November 15, 2024 at 7:32 PM
Check out the new work from the MosSI lab in collaboration with @aidanfoo.bsky.social @laurabrettell.bsky.social @evaheinz7.bsky.social and heaps of others.
MosAIC: An annotated collection of mosquito-associated bacteria with high-quality genome assemblies
journals.plos.org/plosbiology/...
MosAIC: An annotated collection of mosquito-associated bacteria with high-quality genome assemblies
journals.plos.org/plosbiology/...
Reposted by Aidan Foo, PhD
Incredible graphic - the myriad of ways that bacteria defend themselves against antibiotics.
14 resistance mechanisms, summarised by Idan Yelin & Roy Kishony in Cell
www.sciencedirect.com/science/arti...
14 resistance mechanisms, summarised by Idan Yelin & Roy Kishony in Cell
www.sciencedirect.com/science/arti...
November 13, 2024 at 12:46 PM
Incredible graphic - the myriad of ways that bacteria defend themselves against antibiotics.
14 resistance mechanisms, summarised by Idan Yelin & Roy Kishony in Cell
www.sciencedirect.com/science/arti...
14 resistance mechanisms, summarised by Idan Yelin & Roy Kishony in Cell
www.sciencedirect.com/science/arti...