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Pauline Scanlan

@paulinedscanlan.bsky.social
465 followers 388 following 13 posts

School of Microbiology and APC Microbiome Ireland, University College Cork 🇮🇪 Microbial Ecology | Microbial Evolution | Gut Microbiome

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Reposted by Pauline Scanlan
David Bikard @dbikard.bsky.social · 21/09/2026
New paper from the lab, out in Nature Microbiology. We ran CRISPRi screens to ask what genes E. coli needs in order to live in a gut and what this can tell us about the gut environment itself. doi.org/10.1038/s41564-026-02471-8
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Microbiology Society @microbiologysociety.org · 16/09/2026
Quantitative comparison of fungal genome assembly strategies using short and long reads from simulated and empirical sequencing data. Published Open Access and fee-free in MGen using a Publish and Read agreement: doi.org/10.1099/mgen.0.001824 #MGen #PublishandRead
Fig. 1.
Assembly quality metrics for single assembly strategies.
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Alan McNally @alanmcn1.bsky.social · 07/09/2026
10 years at UoB today. The best thing I have ever done career wise. And now just 3 more weeks until the next (and definitely final) big move to @manchester.ac.uk and the amazing @mermanchester.bsky.social as Chair of Microbial genomics
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Seth Bordenstein @symbionticism.bsky.social · 05/09/2026
Fancy relative abundance measurements in your sequencing analyses and yet know there’s a problem with that? Our very own @inschool4life.bsky.social hammers this message and offers a robust solution. @psumbiome.bsky.social youtu.be/2KGJumvaKz0?...
youtu.be
Beyond Compositionality: Scale-Reliant Inference and ALDEx3 for Microbiome Data | Justin Silverman
YouTube video by One Health Microbiome Center at Penn State
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Parody Nigel Farage @parodypm.bsky.social · 05/09/2026
I for one have had enough of people who can barely speak English, living on benefits, ignoring our laws and wearing weird clothes that cover up their faces. So it was disappointing to see a few hundred of them gathered in Dover today.
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Pauline Scanlan @paulinedscanlan.bsky.social · 04/09/2026
congrats to the inimitable @adtsaousis.bsky.social on a brilliant #Blastocystis2026. Thanks to @costprogramme.bsky.social for supporting the @blastocystiscost.bsky.social initiative and faciltating #scientificexcellence & #communitybuilding @apcmicrobiomeirel.bsky.social @uccmicrobiology.bsky.social
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womensartbluesky.bsky.social @womensartbluesky.bsky.social · 03/09/2026
Georgia O'Keeffe, Blue Wave Maine, 1926 #WomensArt
Semi abstract or stylised artwork featuring a white wave in a blue sea
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Johannes Cairns @jcairns.bsky.social · 06/07/2026
Final version is out! 🎉 Community state shifts driven by total carbon availability over resource complexity in a synthetic microbial community In ISME Communications with @teppo-h.bsky.social and coauthors. academic.oup.com/ismecommun/a...
academic.oup.com
Community state shifts driven by total carbon availability over resource complexity in a synthetic microbial community
Abstract. Even though complex microbial communities are ubiquitous and provide essential services for natural and human-associated ecosystems, our knowledg
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Reposted by Pauline Scanlan
Tominaga K. (tomiken) @pacyc184.bsky.social · 31/08/2026
Phage therapy: from basic biology to clinical application | Nature Reviews Microbiology
nature.com
Phage therapy: from basic biology to clinical application - Nature Reviews Microbiology
In this Review, Iredell and colleagues examine key aspects of phage biology and their relevance to phage therapy, and outline current approaches for clinical application of phages, along with their associated challenges.
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Rebecca J Hall @drrebeccajhall.bsky.social · 21/08/2026
#MENI2026 was brilliant. Excellent talks, posters, and discussions. Thanks @siderophile.bsky.social @paulinedscanlan.bsky.social for the invite and for organising such a great event!
A green notebook with ‘Hand bound by Duffy Bookbinders, Dublin, Ireland’s oldest bindery’ on the cover
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Siobhán O'Brien @siderophile.bsky.social · 21/08/2026
And that’s a wrap on #MENI2026! What a great day of microbial evolution research, and a pleasure to host at Trinity with @paulinedscanlan.bsky.social
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Rebecca J Hall @drrebeccajhall.bsky.social · 20/08/2026
Looking forward to a full day of microbial evolution today! I’ll be talking this morning about evolution of AMR from my work with @alanmcn1.bsky.social
Poster that reads ‘Microbial Evolution Network Ireland’
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Arvid Ågren @arvidagren.bsky.social · 04/06/2026
Much has been written about The Selfish Gene, and few books have been both as influential and as persistently contested. To commemorate its 50th anniversary, here are some brief thoughts in the latest issue of @science.org. www.science.org/doi/10.1126/...
science.org
A provocative view of evolution turns 50
The Selfish Gene continues to challenge readers half a century later
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Ran Blekhman @blekhman.bsky.social · 16/06/2026
Nine (not so simple) steps: a practical guide to using machine learning in microbial ecology Step 1: Determine whether machine learning is necessary or even worth doing journals.asm.org/doi/10.1128/...
journals.asm.org
Nine (not so simple) steps: a practical guide to using machine learning in microbial ecology | mBio
Microbial ecologists are increasingly turning to machine learning (ML) models to better identify and predict meaningful biological patterns and relationships in molecular microbial community data (inc...
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Ákos T Kovács @evolvedbiofilm.bsky.social · 16/06/2026
See several blog posts by @paulbrainey.bsky.social 🤔 e.g. The demand behind predatory publishing academicrenewal.substack.com/p/the-demand... 👇🧵 [1/5]
academicrenewal.substack.com
The demand behind predatory publishing
How predatory publishing led to academic renewal
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Ville Friman @frimanscience.bsky.social · 12/06/2026
Very happy that this piece of research finally sees the daylight! Super nice collaboration between Nanjing, York and Helsinki. Fun fact: we started this work over 10 years ago when I was working as a fellow at Imperial College. Sometimes good things come to those who wait.
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Lily Khadempour @khadlily.bsky.social · 09/06/2026
Do you study human microbiomes? Have you used the word "commensal"? Then this paper was written with you in mind! It was an absolute pleasure to write this with the incomparable @ginalewin.bsky.social journals.asm.org/doi/10.1128/...
journals.asm.org
mGem: Tapping into the language of symbiosis to advance human microbiome research | mBio
An overarching goal in microbiome research is to understand how the complex communities in our bodies contribute to health and disease, and ultimately, we aim to leverage and control these communities...
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Michael Baym @baym.lol · 28/05/2026
This is very cool: a simple statistical test of dysbiosis, or really any microbiome composition data relative to a reference. Outperforms Bray-Curtis and every other metric, while simultaneously being very simple to compute. Probably would work on RNAseq data too.
Three ROC curves showing RPD outperforming BCD for each dataset
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Cedric Feschotte @cedricfeschotte.bsky.social · 28/05/2026
Wrote a short piece on Transposable Elements as catalysts of evolutionary innovation for a forthcoming special issue of @naturerevgenet.bsky.social on, duh, Evolutionary Innovation! www.nature.com/articles/s41...
nature.com
Transposable elements as catalysts of evolutionary innovation - Nature Reviews Genetics
In this Comment, Cedric Feschotte highlights evidence from diverse lineages showing that transposable elements are key drivers of evolutionary innovation, repeatedly introducing regulatory and coding ...
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Aude Bernheim @audeber.bsky.social · 22/05/2026
Great piece and cover @science.org about how our field is uncovering the evolutionary and mechanistic connections between bacterial and eukaryotic immunity ! www.science.org/content/article/ancient-wars-between-microbes-gave-us-key-immune-defenses
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Prof Jenny Rohn @jennyrohn.bsky.social · 16/05/2026
Being a PI is an intricate juggling act that requires tough decisions – intellectual, financial, strategic. Yet we are expected to navigate these dangerous waters with very little support. The solo PI model is deeply problematic. My latest blog post #AcademicSky occamstypewriter.org/mindthegap/2...
occamstypewriter.org
In which no scientist is an island – but that’s what we signed up for | Mind the Gap
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Mart Krupovic @mkrupovic.bsky.social · 11/05/2026
With Eugene Koonin, we wrote a rather comprehensive review on the origin, evolution and organization of the #virosphere. We describe all 10 viral realms and the logic behind them, and so much more. Check it out! comptes-rendus.academie-sciences.fr/biologies/ar...
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Daniel Moser @dmoser.bsky.social · 27/04/2026
Pollution levels in Paris after 10 years of advancing sustainable transport.
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Ákos T Kovács @evolvedbiofilm.bsky.social · 18/04/2026
Heterogeneity in microbial antibiotic responses: genetic basis and within-host evolution @cp-trendsgenetics.bsky.social review by Qingyun Liu and Liang-Dong Lyu (吕亮东) www.cell.com/trends/genet...
cell.com
Heterogeneity in microbial antibiotic responses: genetic basis and within-host evolution
Antibiotic response phenotypes have traditionally been classified as either sensitive or resistant. However, accumulating evidence indicates that bacterial responses to antibiotics are far more hetero...
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Anastasios (Tasos) Tsaousis @adtsaousis.bsky.social · 14/04/2026
Many thanks to the @microbiologysociety.org for inviting me to give a talk on #Blastocystis during the #microbio26 in Belfast! It was such a great opportunity to share the work of our @blastocystiscost.bsky.social as well! @costprogramme.bsky.social
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Vaughn Cooper @vscooper.micropopbio.org · 13/04/2026
🆒 new pub! Rapid evolution of Klebsiella pneumoniae biofilms in vitro -> adaptations selected during infection by @gretazabo.bsky.social & Linus Sandegren *hypermucoidy evolves via 📈c-di-GMP, overlaps w/ mutations in UTI and wound isolates. *pleasure to advise this! www.nature.com/articles/s41...
nature.com
Rapid evolution of Klebsiella pneumoniae biofilms in vitro delineates adaptive changes selected during infection - Nature Communications
Biofilm formation on implanted medical devices facilitates infection by the pathogen Klebsiella pneumoniae. Here, Zaborskytė et al. use experimental evolution to show that the bacteria rapidly evolve ...
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APC Microbiome Ireland @apcmicrobiomeirel.bsky.social · 10/04/2026
How should new #Blastocystis subtypes be named? A new @cp-trendsparasitol.bsky.social forum paper argues for minimum standards, incl. near full-length SSU rRNA data & replication, to keep subtype naming stable across studies. With @paulinedscanlan.bsky.social #Parasitology 📰 buff.ly/PVvtrxO
Blastocystis research has grown rapidly with molecular tools, especially next-generation sequencing, increasing subtype discovery but raising methodological and taxonomic challenges. We assess subtype designation criteria, caution against lowering divergence thresholds without biological evidence, and propose minimum standards requiring near full-length small subunit ribosomal RNA data and replication to ensure nomenclatural stability and epidemiological comparability.
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George Conway ⚖️🇺🇸 @gtconway.bsky.social · 04/04/2026
This is absolutely fantastic. ht: @maddenifico.bsky.social
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Sebastian Schmidt @tsbschm.bsky.social · 03/04/2026
Our work on 'hidden diversity' in unbinned contigs is now published in @natmicrobiol.nature.com : www.nature.com/articles/s41... See the linked threads for more details!
nature.com
Unbinned contigs expand known diversity in the global microbiome - Nature Microbiology
Re-analysis of over 92,000 metagenomes reveals hundreds of thousands of previously undescribed Bacterial and Archaeal clades hidden in plain sight.
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Glen O'Hara @gsoh31.bsky.social · 03/04/2026
It's me in the Financial Times, detailing the deep and pernicious influence of one-size-fits-all management consultancy in our universities... Take a look! 👇 www.ft.com/content/5032...
ft.com
Management consultants are ruining UK universities
Relentless off-the-peg commercial rewiring has undermined British higher education
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Pauline Scanlan @paulinedscanlan.bsky.social · 02/04/2026
Thanks to @siderophile.bsky.social for an excellent seminar today @uccmicrobiology.bsky.social showcasing how multiple stressors effect the ecology and evolution of soil microbes thanks to @microscrum.bsky.social for organising!
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MEEhubs @meehubs.bsky.social · 18/03/2026
MEEHubs2026 registration and abstract submission is now online! 🚨🦠✨ Join us Aug 3 - 5, 2026 at one of the 7 hubs or online. We are incredibly excited about our lineup of speakers, and hope that you submit an abstract to contribute too! More information and registration links at: meehubs.org
meehubs.org
Home
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Vivek Mutalik @vivekmutalik.bsky.social · 15/03/2026
New paper 🔔 Collaboration @sullivan-lab.bsky.social Marissa Gittrich led the work Klebsiella phage biology has focused almost entirely on capsulated strains, but capsule loss is the #1 resistance mechanism under phage predation. We used a naturally acapsular host to reveal the receptor landscape
Bacteriophage data on capsular Klebsiella bacteria barcoded library
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Charles Mullon @charlesmullon.bsky.social · 09/03/2026
With @saramitri.bsky.social, @sonjalehtinen.bsky.social and L. Lehmann we’ve launched the UNIL Center for Theory in Ecology and Evolution @unil.bsky.social🇨🇭 To kick things off, we’re offering short visiting fellowships for theorists in ecology & evolution. Apply & pls RP 😀 tinyurl.com/2wem36zz
unil.ch
Unil center for theory in ecology and evolution (UCTEE) - FBM Unil
Page Unil Center for Theory in Ecology and Evolution of site Faculty of Biology and Medicine hosted by the University of Lausanne
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Lilly Cummins @lillycummins.bsky.social · 02/03/2026
I’ve spent a lot of time over the past two years thinking about genome evolution and how recent research revealing complex gene-gene interactions has complicated traditional ‘gene-centric’ genomic approaches to evolution. So here is a review that consolidates these thoughts! rdcu.be/e6pHY
rdcu.be
Epistasis and co-adaptation in bacterial genome evolution
Nature Reviews Genetics - Bacterial genome evolution is shaped by epistasis, which can constrain or promote specific evolutionary paths. The authors review how integrating the effects of epistatic...
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Rafal Mostowy @rafalmostowy.bsky.social · 26/02/2026
📢 Hiring a Postdoc in Computational Phage Biology (Kraków, Poland) We study the evolution & structural modularity of prophage-encoded glycan-degrading enzymes in Klebsiella pneumoniae — combining genomics and AlphaFold-based analyses. Details in attached PDF 👇
docs.google.com
Postdoc Ad
Postdoctoral Position in Computational Phage Biology Microbial Genomics Group, Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Kraków PL Summary We are seeking a postdoctoral rese...
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Zamin Iqbal @zaminiqbal.bsky.social · 26/02/2026
Courtesy of @martibartfast.bsky.social , we have a new release of AllTheBacteria which adds another 322,920 assemblies, covering all ENA (illumina, isolate) prokaryotes to May 2025. allthebacteria.readthedocs.io/en/latest/ov...
allthebacteria.readthedocs.io
Overview — AllTheBacteria documentation
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STCmicrobeblog @stcmicrobeblog.bsky.social · 22/02/2026
here is a comprehensive history of the use of agar in microbiology by corrado nai 👇 🙏 thx for pointing this out @microbingle.bsky.social earlier, corrado told the story of fanny angelina hesse in STC. #MicroSky
smallthingsconsidered.blog
Have you ever heard of Fanny An­gelina Hesse?
by Corrado Nai — A graphic novel about this forgotten woman in science is on its way – but it's unlikely to make an impact without the strong support from the microbiology community. If you have n…
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Sean Gibbons 🦠💩 @gibbological.bsky.social · 19/02/2026
Our latest is out today in @plosbiology.org: "Metabolic modeling reveals determinants of prebiotic and probiotic treatment efficacy across multiple human intervention trials" @isbscience.org @uwbioe.bsky.social @uwgenome.bsky.social doi.org/10.1371/jour...
doi.org
Metabolic modeling reveals determinants of prebiotic and probiotic treatment efficacy across multiple human intervention trials
Prebiotic and probiotic interventions can induce therapeutically relevant shifts in the human microbiome, but their effects are variable across individuals. This study shows that metabolic models can ...
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Research Ireland @researchireland.ie · 19/02/2026
Research Ireland, alongside the Embassy of France in Ireland, has today announced 15 new research partnerships under the Ulysses programme, supporting collaboration between researchers based in Ireland and France. Read more: www.researchireland.ie/news/ulysses...
H.E. Céline Place, the French Ambassador to Ireland, with Research Ireland CEO, Dr Diarmuid O'Brien
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Siobhán O'Brien @siderophile.bsky.social · 18/02/2026
MENI is back! Join us in Dublin this August 2026 for our 3rd Meeting for Microbial Evolution in Ireland. We are delighted to have @rachelmwheatley.bsky.social @drrebeccajhall.bsky.social @jpjhall.bsky.social and @tweethinking.bsky.social join us as keynote speakers this year. miniurl.com/MENI
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Journal of Evolutionary Biology @jevbio.bsky.social · 17/02/2026
Individuals can fall apart into their constituent parts via evolutionary reversions in individuality, but this process can occur in two distinct ways that shape the evolution of individuality: doi.org/10.1093/jeb/... @martijnschenkel.bsky.social, @arvidagren.bsky.social & Manus Patten
doi.org
Evolutionary transitions and reversions in individuality
Abstract. Biological individuality exists in different forms—unicellular, multicellular, colonial, etc.—which have arisen through evolutionary transitions
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Max Fels @mfels.bsky.social · 17/02/2026
The giant viruses surprised us at almost every turn of this project, but ultimately led us down a very rewarding path. Happy to share this work is now available online 🧪
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Michael Brockhurst @brockhurstlab.bsky.social · 14/02/2026
What’s holding back clinical use of phage therapy in the UK? Our workshop last year brought together international experts, biotech and regulators to find out Meeting Report out now in Nature Microbiology with our take on the challenges and opportunities facing the UK phage therapy sector
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School of Microbiology UCC @uccmicrobiology.bsky.social · 06/02/2026
📣We are delighted to share that Jill O’Sullivan’s paper, “Host-microbe multi-omics and succinotype profiling have prognostic value for future relapse in patients with inflammatory bowel disease” (Gut Microbes), has been awarded the 2025 Professor Gerald Fitzgerald Research Award. 🎆
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Ricardo León-Sampedro @rleonsampedro.bsky.social · 05/02/2026
New #BehindThePaper for our latest paper in @natcomms.nature.com (rdcu.be/e2qMK) Secret Invasion: Strain Fate Across Microbiomes Cover illustration by Helena Klein (@illuzation.bsky.social). communities.springernature.com/posts/secret...
communities.springernature.com
Secret Invasion: Strain Fate Across Microbiomes
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Ed Feil @edfeil.bsky.social · 07/01/2026
It has been a long road, but our paper on Klebsiella plasmids is finally out in Lancet Microbe. Thanks to all co authors but especially Marjorie Gibbon and Natacha Couto www.sciencedirect.com/science/arti...
sciencedirect.com
Convergence and global molecular epidemiology of Klebsiella pneumoniae plasmids harbouring the iuc3 virulence locus: a population genomic analysis
Klebsiella pneumoniae is an important pathogen of humans and animals. In the past five years, increasing reports of convergent strains that carry both…
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Professor Lesley Hoyles @bugsinyourguts.bsky.social · 06/01/2026
🧬 Free @microbesng.bsky.social PopUp ECR symposium 🧬 UK-based MRes or PhD student, research assistant or postdoc working on microbial genomics or metagenomics? Present your work and/or chair a session, plus excellent keynote speakers: @halllab.bsky.social and @alexmsalmeida.bsky.social. #MNGPopUp
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Hall Lab @halllab.bsky.social · 07/01/2026
Happy New Year – new role! 🎉 We’re looking for a PostDoc to join us in @halllab.bsky.social @unibirmingham.bsky.social. Full-time, fixed-term to March 2028. Note tight closing date: 11 Jan 2026. CV + cover letter (submit via portal). Further details 👇 edzz.fa.em3.oraclecloud.com/hcmUI/Candid...
edzz.fa.em3.oraclecloud.com
Research Fellow - Department of Microbes, Infection and Microbiomes - 106849 - Grade 7
To create and contribute to the creation of knowledge by undertaking a specified range of activities as part of an Investigator project funded by Wellcome, focusing on understanding microbial and diet...
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