Daniel Figeys

Daniel Figeys

@dfigeys.bsky.social

Precision-function-based microbiome trials. Ex vivo microbiome assays. Microbiome–xenobiotic interactions. Meta-omics analyses

393 followers706 following44 posts

Daniel Figeys reposted

🆕 Vacancy! We’re looking for a Postdoctoral Research Scientist to investigate relationships between diet, the human gut microbiome and mental health across more than 20 European cohorts within the NUTRIMIND consortium 💷 £39,000 to £46,500 🗓️ Apply by 17 November 2026 ➡️ buff.ly/lh4ZBr0

Daniel Figeys reposted

“I’m delighted to announce Stella’s appointment as Chair from next year. Stella’s skills and experience are perfectly aligned with Quadram Institute Bioscience’s mission to bring real health and economic benefits to our society in the years ahead." 💬Our Director Professor @dfigeys.bsky.social

buff.lyQuadram Institute Bioscience announces appointment of a new Chair of Trustees - Quadram InstituteProfessor Anne Ferguson-Smith, BBSRC Executive Chair, said: “I am delighted to welcome Stella Peace as the new Chair of the Board of Trustees at Quadram Institute Bioscience. Stella brings a highly…

Daniel Figeys reposted

Replying to @wcratcliff.bsky.social

3/17 Graduate students and postdocs: we strongly encourage you to apply! The Gordon Research Seminar (GRS), organized by Noah Houpt (@noahhoupt.bsky.social) and Duhita Sant (@duhitasant.bsky.social), runs June 26–27, immediately before the GRC.

grc.org2027 Microbial Population Biology (GRS) Seminar GRCThe 2027 Gordon Research Seminar on Microbial Population Biology (GRS) will be held in Andover, New Hampshire. Apply today to reserve your spot.

Daniel Figeys reposted

This Trustee Director role is an exciting opportunity to have significant impact on our organisation in a unique partnership between science, academia and health research, as the Institute enters a phase of significant growth and increased global impact 🗓️ Apply by 31 August 2026 ➡️ buff.ly/zmfgJLL

Wu, Zhang et al. introduce MetaTree, a browser-based platform for hierarchical data visualisation, multi-group comparison with statistical analysis. Easy to use and publication ready figures. #microbiome + #metaproteomics. doi.org/10.1186/s128...

doi.orgMetaTree: an interactive web platform for aligned hierarchical data visualization and multi-group comparison - BMC BioinformaticsBackground Hierarchical quantitative profiles are widely used in microbiome studies and other domains. However, comparing multiple samples and experimental groups while preserving hierarchical structure remains challenging. Many existing workflows require extensive manual figure assembly or do not support aligned comparisons across conditions on a shared hierarchy. Results We developed MetaTree, an open-source platform that runs in a web browser for interactive visualization and comparative analysis of hierarchical quantitative data. MetaTree anchors samples, groups, and contrasts between groups to a shared reference hierarchy, preserving one-to-one node correspondence so that the same clade is compared in the same position across views. In addition to visualization, MetaTree integrates statistical testing for comparisons between two groups with false discovery rate (FDR) control, enabling users to identify clades with consistent differences between conditions and interpret them in hierarchical context. MetaTree also provides user configurable controls for visual encoding, filtering thresholds, label density, and layout, allowing figures to be adapted to different datasets and reporting needs. The interface remains usable for large hierarchies through interactive navigation, adaptive label handling, and branch collapsing. Conclusions MetaTree is an installation-free web platform (https://byemaxx.github.io/MetaTree) for topology-consistent visualization and comparison of hierarchical profiles, supporting coordinated multi-panel exploration and automated comparison matrices to enable rapid generation of publication-ready figures for microbiome and other hierarchical datasets.

Daniel Figeys reposted

Across three studies, one message is clear: prebiotics are not one-size-fits-all. Fibre structure shapes the microbial functions activated, while each person’s microbiome determines the strength of the response and the metabolites produced.

Different fibres, different microbiomes and different microbial routes. However, dietary carbohydrates consistently redirect microbial activity away from host mucin and towards fibre utilisation. Across fibres, we observed broader changes in microbial enzymes, cross-feeding and metabolites.

Dobranowski et al. studied the response of 66 paediatric IBD microbiomes to nine resistant starches. The results were highly personalised, while multi-omics uncovered metabolites beyond butyrate and a shift from mucin degradation to starch utilisation. www.nature.com/articles/s41...

nature.comIndividual variability shapes ex vivo responses to resistant starch in inflammatory bowel disease derived microbiomes - npj Biofilms and Microbiomesnpj Biofilms and Microbiomes - Individual variability shapes ex vivo responses to resistant starch in inflammatory bowel disease derived microbiomes

Our earlier work with six structurally distinct oligosaccharides showed that microbiomes share broad responses—such as prioritising dietary fibre over mucin—but the microbes and enzymes involved can differ markedly between individuals. www.nature.com/articles/s41...

nature.comMicrobiome-dependent functional responses to structurally distinct oligosaccharides revealed by metaproteomics - npj Biofilms and Microbiomesnpj Biofilms and Microbiomes - Microbiome-dependent functional responses to structurally distinct oligosaccharides revealed by metaproteomics

Tired of long lists of possible bacteria with little statistical support in metaproteomics? Wu et al. developed MetaUmbra which provides statistically evidence on which bacteria are present in a microbiome. doi.org/10.64898/202... #microbiome #metaproteomics #bioinformatics #proteomics

Daniel Figeys reposted

⏰ Closing soon We’re looking for a Research Scientist (Metaproteomics) to join Dr Kai Cheng's group to develop and apply computational and analytical methods for metaproteomics 💻️ 💷 £37,500 to £45,350 🗓️ Apply by 6 May ➡️ buff.ly/8sZPg1T

Daniel Figeys reposted

"Tell me who your friends are, and I’ll tell you who you are." It turns out, microbes follow the same rule! Very proud to share our lab's new paper in @natmicrobiol.nature.com showing that bacteria don't just respond to their environment, they respond to each other. www.nature.com/articles/s41...

nature.comCommunity context reshapes microbial proteomes and reduces functional overlap - Nature MicrobiologyBiotic interactions modulate protein abundance, reducing functional redundancy and increasing productivity in complex bacterial communities.

Daniel Figeys reposted

Great to hear our local MP Ben Goldsborough highlighting in Parliament the world-class science taking place here at the Quadram Institute and @johninnescentre.bsky.social on vitamin D deficiency and sunshine tomatoes🍅 We’d be delighted to host a visit by Dame Angela Eagle.

Ben Goldsborough MP@bengoldsborough.bsky.social

One in five people face Vitamin D deficiency. In South Norfolk, we are part of the solution. At the @quadraminstitute.bsky.social, @johninnescentre.bsky.social located at the Norwich Research Park, scientists are testing Vitamin D rich tomatoes. Learn more: quadram.ac.uk/vital-d/

Daniel Figeys reposted

Daniel Figeys reposted

Daniel Figeys reposted

⏰ Closing soon! We’re looking for an ambitious and collaborative Group Leader or Career Track Group Leader to pioneer the development of next-generation microbiome assays and model systems 💷 Competitive 🗓️ Apply by 15 February 2026 ➡️ buff.ly/W3Sphca

Exploring #microbiome data? MetaTree makes statistically based hierarchical tree comparisons easy and accessible.

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social

MetaTree: an interactive web platform for hierarchical data visualization and multi-group comparison https://www.biorxiv.org/content/10.64898/2026.01.22.701099v1

If you have experience in #metaproteomics and microbiology, then this is for you!

Quadram Institute@quadraminstitute.bsky.social

🆕 Vacancy! We are looking for a Senior Research Scientist to support with day-to-day running of @dfigeys.bsky.social lab, including line management of staff, overseeing budgets, and leading the scientific direction. 💷 £45,450 to £56,750 🗓️ Apply by 15 February 2026 ➡️ buff.ly/UpcuEPa

Daniel Figeys reposted

⏰ Closing soon! We are looking for a Group Leader with a focus on nutrition and microbiome-based interventions for the prevention and management of obesity to join our Food, Microbiome and Health research programme as a Group Leader. 💷 Competitive 🗓️ Apply by 18 January 2026 ➡️ buff.ly/5CIkq6J

Zhang et al, with the #RapidAIM assay and #metaproteomics, show that gut #microbiomes exhibit shared and individualized functional responses when exposed to six structurally distinct oligosaccharides. Functional understanding requires studying in dividual microbiome. www.nature.com/articles/s41...

nature.comMicrobiome-dependent functional responses to structurally distinct oligosaccharides revealed by metaproteomics - npj Biofilms and Microbiomesnpj Biofilms and Microbiomes - Microbiome-dependent functional responses to structurally distinct oligosaccharides revealed by metaproteomics

Daniel Figeys reposted

“The Quadram Institute is proud to be part of the newly launched National Research Organisations (NRO) Group – uniting UK research centres to #MakingResearchMatter for people, communities & the economy." 💬 Professor @dfigeys.bsky.social

NRO Group@nro-group.bsky.social

We’ve launched! 🎉 The National Research Organisations (NRO) Group unites 35 UK research organisations to provide a unified and authoritative perspective on science, policy, and research investment. Learn more: nrogroup.org #MakingResearchMatter #NROGroup

Daniel Figeys reposted

🆕 Anti-depressant drugs cause profound changes to the human gut microbiome, but these changes could be mitigated by prebiotics, according to a major new survey of how the microbial community in the gut responds to different therapeutic drugs 💊 @dfigeys.bsky.social buff.ly/uKd5PDv

buff.lyPrebiotics reverse effects of anti-depressants on the gut microbiome - Quadram InstituteScientists from the University of Ottawa and Beijing Institute of Lifeomics found that SSRIs, SNRIs and Tricyclic Antidepressants, commonly prescribed anti-depressants that target the…

Daniel Figeys reposted

Functional redundancy matters: the more overlapping microbial functions you have, the more resilient your #microbiome. We showed a strong negative correlation between redundancy loss and increase in #antimicrobial resistance protein upon #drug treatment of microbiomes. @quadraminstitute.bsky.social

Daniel Figeys@dfigeys.bsky.social

Interested in #drugs, #microbiome and #antibiotic resistance, then check out our paper on the effects of over 300 drugs on the gut microbiome. Exciting results as well on the role of antibiotic resistance defining how microbiomes respond to drugs. @quadraminstitute.bsky.social rdcu.be/eMmcT

Interestingly, #drugs for the nervous system (antidepressants/antipsychotics) stand out: #SSRI/ #SNRI/ #TCA push the gut #microbiome into alternate states, lowering functional redundancy(lower capacity to respond) and ramping up antimicrobial-resistance proteins. @quadraminstitute.bsky.social

Daniel Figeys@dfigeys.bsky.social

From #drug cabinet → gut #microbiome: screening 312 therapeutic compounds, we mapped 4.6 million microbial protein-level responses to reveal how our drugs don’t just target us, they hit our gut microbes too. rdcu.be/eMmcT

Daniel Figeys reposted

1 in 5 people in the UK are estimated to be deficient in #vitaminD during winter and spring 📉 Our ViTaL-D Study aims to understand whether tomatoes biofortified through gene-editing tomatoes to be high in vitamin D leads to higher levels of active vitamin D in the blood 🍅 ➡️ buff.ly/SIsELo6

Daniel Figeys reposted

Daniel Figeys reposted

“This study is particularly important to me as it took place during my post doc years at the @uniofeastanglia.bsky.social and it has been a source of inspiration for my current research line, as a newly appointed Early Career Fellow at the Quadram Institute." 💬 Dr Serena Monaco

buff.lyNew technique to speed up the design of drugs targeting proteins in the cell membrane - Quadram InstituteAn team has developed a new technique that will speed up the design of drugs targeting ion channels, a type of cell membrane protein

Daniel Figeys reposted

“Vitamin D deficiency represents a significant public health concern, especially during the winter months with significant deficiency across the UK population." 💬 Professor Martin Warren, our Chief Scientific Officer

buff.lyVitamin D3 concentrations are lowered by common vitamin D supplement - Quadram InstituteTaking vitamin D2 might be lowering the body's levels of the more efficient form of vitamin D, vitamin D3, according to new research

Daniel Figeys reposted

This is an exciting position that will shape the direction of how we target the gut microbiome. Come join my lab at the Quadram Institute.

Quadram Institute@quadraminstitute.bsky.social

🆕 Vacancy! We're looking for a Senior Research Scientist to advance precision prebiotic microbiome intervention trials to study the interactions of prebiotics, drugs and other xenobiotics on the gut microbiome. 💷 £45,450 to £56,750 🗓️ Apply by 2 October 2025 ➡️ buff.ly/BQKamDW

Interested in compound- microbiome interactions, and how they affect health? Join my lab at the Quadram Institute.

Quadram Institute@quadraminstitute.bsky.social

🆕 Vacancy! We're looking for a Research Scientist (Xenobiotics) to investigate xenobiotic–microbiome interactions and understand the variation in responses across different individual microbiomes. 💷 £37,500 to £45,350 🗓️ Apply by 2 October 2025 ➡️ buff.ly/8abEye5