Aidan Foo, PhD

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 ...

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....

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...

Emerging models to study competitive interactions within bacterial communities www.cell.com/trends/micro... #jcampubs

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

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]🧵

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...

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

Home A tool for generating consensus long-read assemblies for bacterial genomes - rrwick/Autocycler

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)

Phylogenetic and functional diversity among Drosophila-associated metagenome-assembled genomes http://biorxiv.org/cgi/content/short/2024.12.19.629488v1

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, ...

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/...

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...

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/...

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...

relevant to a paper I just reviewed (and cited this paper bmcbiol.biomedcentral.com/articles/10....). Ppl seem resistant to this lesson...

An eco-evolutionary perspective on antimicrobial resistance in the context of One Health Health sciences; Biological sciences; Microbiology; Evolutionary biology

A collaborative perspective on eco-evolutionary dynamics of antimicrobial resistance in the context of One Health.

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

Thank you! And thank you for being a wonderful examiner ☺️ it was a fantastic experience

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...

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

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

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/...

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 ...

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

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...

Bifidobacteriaceae diversity in the human microbiome from a large-scale genome-wide analysis https://pubmed.ncbi.nlm.nih.gov/39602306/

Thanks Eva 😊

Lots of MosSI Lab representation at the LSTM 125th Scientific Symposium this week!

@mosquitomicrobe.bsky.social spoke about our Anopheles Wolbachia work.

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...

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

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?

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

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!

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/...

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...