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Abish Stephen

@astephen.bsky.social
328 followers 521 following 76 posts

Microbiologist at Queen Mary University of London. I work on anaerobes, biofilms, host-microbial models, bacterial volatile metabolites and oral microbiota-systemic axis. Passionate about guitars, motorsport and cricket. #bikerlife Views my own.

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Reposted by Abish Stephen
Bahtiyar Yilmaz @bahtiyil.bsky.social · 03/08/2026
A stool transplant delivers billions of microbes into a sick gut. Almost none move in for good. We followed donor-recipient pairs from whole communities down to single nucleotides, and found the gut runs a ruthless strain-level filter. Out now in Cell Reports 🧵 www.cell.com/cell-reports...
cell.com
Strain-level ecological filtering governs microbial colonization of the human gut
Baertschi et al. demonstrate that microbiota transplantation functions as a selective ecological filter. Although donor species frequently appear, only specific lineages achieve stable strain integrat...
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Queen Mary University of London @qmul.bsky.social · 03/08/2026
Queen Mary has received a £1.3m Wolfson Foundation grant to establish a Health and Pollution Research Hub. Led by Dr Vahitha Abdul Salam and Dr Abish Stephen, the Hub will explore how pollution impacts health. Read more: www.qmul.ac.uk/news/latest-...
qmul.ac.uk
Queen Mary awarded prestigious grant to better understand links between pollution and health
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Abish Stephen @astephen.bsky.social · 10/06/2026
Very pleased to share this paper from Esme McPolin-Hall's PhD project. I was involved from the microbiology side, and it’s a very cool Staphylococcus–Cutibacterium–Malassezia story about #dandruff, dysbiosis and host signalling. 🧫🍄 1/ academic.oup.com/bjd/advance-...
academic.oup.com
Engineering microbial symbiosis and dysbiosis reveals a new AhR-mediated mechanism underlying dandruff pathogenesis
Microbial dysbiosis of the scalp microbiome drives dandruff-like phenotypic changes in a microbially-competent 3D skin organotypic model, including impaire
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bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 04/06/2026
Supraphysiological Estradiol During Ovarian Stimulation Reveals Microbiome Resilience and Prevotella Opportunism www.biorxiv.org/content/10.64898/20…
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Nature Microbiology @natmicrobiol.nature.com · 13/03/2026
#NatMicroPicks Antibiotics in the long run ⌛💊🦠 Antibiotic use shows lasting associations with reduced gut microbial diversity for up to 8 years, indicating long-term impacts on the adult gut microbiome. #MicroSky #MicrobiomeSky www.nature.com/articles/s41...
nature.com
Antibiotic use and gut microbiome composition links from individual-level prescription data of 14,979 individuals - Nature Medicine
Using individual-level data from the Swedish Prescribed Drug Register and fecal metagenomes of 14,979 individuals in Sweden, the authors examined the association between oral antibiotic use over 8 yea...
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Reposted by Abish Stephen
Páll Melsted @pmelsted.bsky.social · 06/03/2026
Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data. The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv www.biorxiv.org/content/10.6... and github github.com/pachterlab/k... Figure 1 shows they key result
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Prof Gavin Yamey MD MPH @gavinyamey.bsky.social · 06/03/2026
I think it was a mistake to put right-wing hot-take podcasters in charge of the FDA, NIH, CDC, and CMS—the so-called “MAGA podcaster to policy pipeline”
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Prof Danny Altmann @daltmann.bsky.social · 05/03/2026
Immune cells from the gut drive development of Parkinson’s disease in the brain www.nature.com/articles/d41...
nature.com
Immune cells from the gut drive development of Parkinson’s disease in the brain
In ‘body-first’ Parkinson’s disease, misfolded proteins propagate from the gut’s nervous system to the brain. Immune-cell activity seems to play a key part in this spread.
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Debnath Ghosal @debnathghosal.bsky.social · 05/02/2026
📣 New paper alert! This is a story of molecular tricks that let spirochetes (spiral-shaped bacteria) drill through tissue. www.biorxiv.org/content/10.6...
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Brian Stevenson Ph.D. spirochete lab @bstevensonlab.bsky.social · 05/03/2026
Structural basis for curvature generation and functional specialization in spirochete flagella #MicroSky
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Abish Stephen @astephen.bsky.social · 04/03/2026
More #PhDOpportunities! This time, developing physiologically relevant models to study dental #erosion. The project combines fluid flow simulation, surface metrology and imaging to understand how #enamel responds to dynamic acid and mechanical challenges. 🦷🌊🧪 Based at @unisouthampton.bsky.social!
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Abish Stephen @astephen.bsky.social · 04/03/2026
Delighted to collaborate on this exciting #PhDOpportunity exploring links between the oral #microbiome and #brain health. This project will investigate how periodontal microbial metabolites influence the #bloodbrainbarrier and neurovascular biology. @drsimonmcarthur.bsky.social 🧠🧪
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Abish Stephen @astephen.bsky.social · 04/03/2026
Excited to advertise a new #PhDOpportunity in my lab at @qmul.bsky.social exploring how oral microbial communities regulate dietary #nitrate metabolism and shape #nitricoxide biology. We’ll combine stable #isotope tracing and #metaomics to nitrate flux in oral #biofilms.🧪 Get in touch if interested!
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AT-OHR @atohr-dtp.bsky.social · 04/03/2026
🦠🧪 #PhDOpportunity Can we weaken dental plaque without killing beneficial microbes? This PhD explores non-biocidal strategies to disrupt oral #biofilm structure, investigating how targeted interventions can destabilise plaque while preserving #microbiome balance. 📍 @glasgowcaledonian.bsky.social
findaphd.com
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AT-OHR @atohr-dtp.bsky.social · 04/03/2026
🔬 Using laboratory and saliva-derived #biofilm models, this project examines how biofilm disruption affects community organisation, stability, and regrowth dynamics compared with conventional #antimicrobials. 🔗 Apply via ATOHR Project led by Dr. Will Johnston
findaphd.com
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AT-OHR @atohr-dtp.bsky.social · 04/03/2026
🔬 Using ex vivo biofilm models and multi-omics, this project investigates how repeated low-level challenges influence microbial structure, stress tolerance, and cross-kingdom dynamics in the oral ecosystem. 🔗 Apply via #ATOHR [2/2]
findaphd.com
Ecological Consequences of Environmental Stressors in Interkingdom Microbial Communities (Reference: SHLS26139-Ramage) at Glasgow Caledonian University on FindAPhD.com
PhD Project - Ecological Consequences of Environmental Stressors in Interkingdom Microbial Communities (Reference: SHLS26139-Ramage) at Glasgow Caledonian University, listed on FindAPhD.com
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Reposted by Abish Stephen
AT-OHR @atohr-dtp.bsky.social · 04/03/2026
🧪 #PhDOpportunity How do microbial communities adapt to everyday challenges? This PhD explores bacterial–fungal interactions in oral biofilms and how environmental stress shapes microbial community behaviour and resilience. 📍 @glasgowcaledonian.bsky.social At Prof. Gordon Ramage's group [1/2]
findaphd.com
Ecological Consequences of Environmental Stressors in Interkingdom Microbial Communities (Reference: SHLS26139-Ramage) at Glasgow Caledonian University on FindAPhD.com
PhD Project - Ecological Consequences of Environmental Stressors in Interkingdom Microbial Communities (Reference: SHLS26139-Ramage) at Glasgow Caledonian University, listed on FindAPhD.com
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Reposted by Abish Stephen
Ran Blekhman @blekhman.bsky.social · 02/03/2026
AI has huge promise for genomics -- but it has consistently failed at microbiome-based prediction. My new post on why simple models keep winning, where deep learning actually earns its place, and where the field is headed blekhman.substack.com/p/ai-keeps-f...
blekhman.substack.com
AI Keeps Failing at Microbiome Prediction
Why simple models keep winning, where deep learning still shines, and where the field is headed
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derek guy @dieworkwear.bsky.social · 27/02/2026
this is what they said it would be like under socialism
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QMUL Centre for Psychiatry & Mental Health @qmulpsychiatry.bsky.social · 24/02/2026
@qmul.bsky.social @bartscharity.bsky.social Doctoral Training Programme - five fully funded 4 year PhD Studentships in Biomedical Research. Closing date for applications: Monday March 16th 2026 Please share - more info here: www.findaphd.com/phds/program...
findaphd.com
FindAPhD : Queen Mary University of London: Barts Charity Doctoral Training Programme at Queen Mary University of London
Apply for a PhD: Queen Mary University of London: Barts Charity Doctoral Training Programme at Queen Mary University of London
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Reposted by Abish Stephen
MwahahahahahadScientist @mads100tist.bsky.social · 25/02/2026
Motion to stop referring to it as Next Generation Sequencing. That's like saying The Matrix is a recent movie
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Derek Lowe @dereklowe.bsky.social · 25/02/2026
I mean, what are you supposed to do with people like this? It’s like saying that you wish your kids could get in some good old-fashioned car crashes without all those seatbelts and air bags.
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Brian Stevenson Ph.D. spirochete lab @bstevensonlab.bsky.social · 25/02/2026
Major advance in T. pallidum reserach: "First human cell-based cultivation system for the syphilis spirochete Treponema pallidum" link.springer.com/article/10.1... #MicroSky
Figure from this publication:
Human foreskin-based cultivation system supports the growth of various
T. pallidum strains (n=8), from the Nichols-like as well as the SS14-like cluster. Note that human foreskin fibroblast cells were prepared as an equal mixture of three tested cell lines. Each T. pallidum strain was cultivated in a single in vitro well, representing a sole experimental replicate used for data acquisition.
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Reposted by Abish Stephen
Simon McArthur @drsimonmcarthur.bsky.social · 24/02/2026
Fully Funded PhD Studentship Opportunity (4 years) at Queen Mary, University of London Why is gum disease a risk factor for dementia? Come and help us find out! 🗓 Application deadline: 15th May 2026 Apply here: tinyurl.com/4xvdzpjs Please share! #Microbiome #Dementia #neuroskyence 🧪 1/3
tinyurl.com
Oral–systemic links: periodontal microbes and the blood-brain barrier at Queen Mary University of London on FindAPhD.com
PhD Project - Oral–systemic links: periodontal microbes and the blood-brain barrier at Queen Mary University of London, listed on FindAPhD.com
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Syma Khalid @sykhalid.bsky.social · 24/02/2026
Come work with Ben Berks FRS in Oxford 2 x PDRA posts: Molecular Analysis of Bacterial Outer Membrane Protein Biogenesis 2 complementary projects investigating bacterial outer membrane protein biogenesis. Building on our recent work (Nature (2015) 647: 479-487) my.corehr.com/pls/uoxrecru...
my.corehr.com
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Dr Duncan Robertson @duncanrobertson.bsky.social · 21/02/2026
Ethics.
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Flo Débarre @flodebarre.eurosky.social · 21/02/2026
Interesting how this scandal involves for real some false claims made about Covid origin: - doing abroad with US funds research not allowed in the US - skipping the evaluation process and having approval straight at the director office As if false accusations were indeed admissions of intent
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Kristian G. Andersen @kgandersen.bsky.social · 18/02/2026
"AGI is just around the corner, which will revolutionize everything. We just need to scale". There you go - that's a $1 trillion plan, $1 billion being peanuts 😉.
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Michael Baym @baym.lol · 18/02/2026
I’m genuinely, unironically impressed at the idea of having a $1b plan to do… anything. A $1m plan is trivial. A $30m plan takes real work. But a priced-out plan with reasonable timelines and expenses that comes to the order of a billion? That’s not easy
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Nature Biotechnology @natbiotech.nature.com · 17/02/2026
Culturing microbiome therapeutics with big data Emerging datasets from large human cohorts are dissecting the underlying mechanisms of microbiome–host interactions and accelerating progress in targeted microbiome therapeutics go.nature.com/4akDuef
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David Emmett @motomatters.com · 14/02/2026
Outstanding thread
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Segata Lab @cibiocm.bsky.social · 12/02/2026
Enjoy reading our "behind the paper" story: www.nature.com/articles/d41...
nature.com
Babies at nursery shape each other’s microbiomes
Strains of commensal gut bacteria spread among babies and their families in a matter of months.
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Alex Grossman @grossmanmicrobio.bsky.social · 12/02/2026
It's funny, my PhD advisor Dr. Goodrich-Blair would also tell stories about those exact lectures. Must have made an incredible impression! I'll do some reading and find out if anything looks like what we see in our episymbionts. I do think we're just about ready to dive into CPR regulation pathways.
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Steve Baker @bakersm11.bsky.social · 11/02/2026
I'm not biophysicist, but the 50 or so pN of energy of a twitch must com from somewhere? As a biochemist, even the mention of a pfk homolog switches my train of thought back to the days of listening to Fredrick Neidhart talk about the "magic spot" pmc.ncbi.nlm.nih.gov/articles/PMC...
pmc.ncbi.nlm.nih.gov
A competence-regulated toxin-antitoxin system in Haemophilus influenzae
Natural competence allows bacteria to respond to environmental and nutritional cues by taking up free DNA from their surroundings, thus gaining both nutrients and genetic information. In the Gram-negative bacterium Haemophilus influenzae, the genes ...
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gramage74.bsky.social @gramage74.bsky.social · 11/02/2026
We would be delighted to receive your applications 🙏🏻
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Abish Stephen @astephen.bsky.social · 11/02/2026
Hey everyone, please welcome Gordon Ramage @gramage74.bsky.social back to #Bluesky and follow! #fungi #microsky #biofilmsky 🧪
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apreston243.bsky.social @apreston243.bsky.social · 06/02/2026
New profile alert! The latest microbial profile in Microbiology, the low down on the recently renamed Candidozyma auris. @microbiologysociety.org @leighannsherry.bsky.social www.microbiologyresearch.org/content/jour...
microbiologyresearch.org
Microbe Profile: Candidozyma auris: an emergent and resilient yeast and new antifungal strategies
Candidozyma auris is an emerging opportunistic yeast that is important because of its multidrug resistance, persistence in healthcare environments and ability to cause outbreaks. Since its discovery i...
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Alex Grossman @grossmanmicrobio.bsky.social · 10/02/2026
That being said, pilin expression and pili-dependent twitching is induced by host exposure. We have quantified piliation of unattached cells (~7 per cell) via CryoEM, however the host cells are so much more electron dense that we could not quantify from an attached cell. 2/2 doi.org/10.1093/isme...
doi.org
Saccharibacteria deploy two distinct type IV pili, driving episymbiosis, host competition, and twitching motility
Abstract. All cultivated Patescibacteria, also known as the candidate phyla radiation, are obligate episymbionts residing on other microbes. Despite being
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Alex Grossman @grossmanmicrobio.bsky.social · 10/02/2026
Hello Steve! I wish I had a better answer for you, we are looking, but we do not know yet how Saccharibacteria are regulating their natural competence. We know they have 2 distinct pili (thick and thin) and a T4SS. The thin pili isn't needed for competence, but the thick pili of T4SS could be? 1/2
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Abish Stephen @astephen.bsky.social · 09/02/2026
Excited for the launch of this #IDLA! 20 PhDs are available in total over the next 3 years! Please look through the project list and get in touch if anything I'm involved in is of interest! 🧪 #spatial #metallomics #nitrate #metabolism #oral-brain-axis #DTP #industry atohr.org/projects
atohr.org
BBSRC-Haleon Industrial Doctoral Partnership
This platform provides comprehensive information about an industrial doctoral partnership, including application details, training opportunities, and project listings.
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Abish Stephen @astephen.bsky.social · 09/02/2026
Bit late to the party...WGS based oral microbiome GWAS makes Nature! Some very cool bacterial functional associations are discussed in the paper. Check it out! www.nature.com/articles/s41... 🧪
nature.com
Human and bacterial genetic variation shape oral microbiomes and health - Nature
Human genetic loci that associate with composition of the oral microbiome are identified using saliva-derived DNA, where the same host genetics also shapes oral health and genetic varia...
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Abish Stephen @astephen.bsky.social · 09/02/2026
Excited for the launch of this #IDLA! 20 PhDs are available in total over the next 3 years! Please look through the project list and get in touch if anything I'm involved in is of interest! 🧪 #spatial #metallomics #nitrate #metabolism #oral-brain-axis #DTP #industry atohr.org/projects
atohr.org
BBSRC-Haleon Industrial Doctoral Partnership
This platform provides comprehensive information about an industrial doctoral partnership, including application details, training opportunities, and project listings.
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AT-OHR @atohr-dtp.bsky.social · 09/02/2026
🚀 We’re launching a new Industrial Doctoral Landscape Award funded by BBSRC in partnership with Haleon. 🎓 Recruiting now for our first PhD cohort (Oct 2026) - to do doctoral research at the interface of academia & industry, tackling real-world challenges aligned with BBSRC priorities.
atohr.org
BBSRC-Haleon Industrial Doctoral Partnership
This platform provides comprehensive information about an industrial doctoral partnership, including application details, training opportunities, and project listings.
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Prof Gavin Yamey MD MPH @gavinyamey.bsky.social · 23/01/2026
One of the most beautiful documents ever created: the leaflet that everyone received when Britain's NHS was launched (1948) "Everyone—rich or poor, man, woman or child—can use it... There are no charges, except for a few special items...it will relieve your money worries in time of illness”
The New National Health Service
Your new National Health Service begins on 5th July. What is it? How do you get it?
“It will provide you with all medical, dental and nursing care. Everyone-rich or poor, man, woman or child – can use it or any part of it. There are no charges, except for a few special items. There are no insurance qualifications. But it is not a “charity”. You are all paying for it, mainly as taxpayers, and it will relieve your money worries in time of illness.”
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Abish Stephen @astephen.bsky.social · 05/01/2026
Ultrasmall episymbiont Nanosynbacter lyticus employs multiple ATP-generating metabolic pathways during horizontal transmission #microsky 🧪 academic.oup.com/ismej/articl...
academic.oup.com
Ultrasmall episymbiont Nanosynbacter lyticus employs multiple ATP-generating metabolic pathways during horizontal transmission
Abstract. Saccharibacteria (formerly TM7) are a group of environmentally diverse, ultrasmall bacteria with highly reduced genomes belonging to Patescibacte
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Onisillos @onisillos.bsky.social · 01/01/2026
This is a very interesting development www.theguardian.com/society/2026...
theguardian.com
Children in England to be offered vaccines in their own homes
Exclusive: Pilot scheme launches as one in five start primary school with no protection against deadly diseases
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BejaLabTechnion @bejalab.bsky.social · 16/11/2025
Characterization of the tumor microbiome of brain metastases and glioblastoma reveals tumor-type-specific and location-specific microbial signatures www.nature.com/articles/s43...
nature.com
Characterization of the tumor microbiome of brain metastases and glioblastoma reveals tumor-type-specific and location-specific microbial signatures - Nature Cancer
Using multiple visualization and profiling methods, Gigi et al. characterize the microbiome diversity of 322 brain tumors including brain metastases and glioblastomas.
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Abish Stephen @astephen.bsky.social · 29/10/2025
Eeek!! www.bbc.com/news/article...
bbc.com
BBC investigation exposes dangerous teeth-whitening industry - BBC News
A BBC investigation finds kits on sale containing more than 500 times the legal limit of bleach.
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BK. Titanji @boghuma.bsky.social · 25/10/2025
Finally read the paper and it's worth the buzz. mRNA vaccines saved 20 million lives in a global pandemic and the technology is opening up new avenues for the treatment of deadly cancers. This is really one of the most impactful scientific developments of our time. www.nature.com/articles/s41...
nature.com
SARS-CoV-2 mRNA vaccines sensitize tumours to immune checkpoint blockade - Nature
mRNA vaccines targeting SARS-CoV-2 also sensitize tumours to immune checkpoint inhibitors.
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Nature Microbiology @natmicrobiol.nature.com · 01/10/2025
#NewResearch Despite being a virulence factor, candidalysin toxin is essential for Candida albicans to penetrate the oral epithelium to establish non-infectious colonisation. @lableibundgut.bsky.social @frois-martins.bsky.social @leibniz-hki.de #MicroSky 🍄 www.nature.com/articles/s41...
nature.com
Dynamic expression of candidalysin facilitates oral colonization of Candida albicans in mice - Nature Microbiology
Despite being a virulence factor, candidalysin toxin is essential for Candida albicans to penetrate the oral epithelium to establish and maintain non-infectious colonization
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