Falk Hildebrand

The human gut microbiome in enteric infections: from association to translation Enteric infections remain a leading global cause of morbidity, mortality and economic loss, increasingly compounded by the rise of antimicrobial resistance. The gut microbiome — spanning bacteria, ...

Our team wrote a review for Gut Microbes on the role of the gut #microbiome in modulating enteric infections. Great team effort by Qi Yin, @samriddhigupta.bsky.social and Efrat Muller: www.tandfonline.com/doi/full/10....

In #Microbiome

🚨Introducing MicroPhrophet: a personalized, temporal‑aware framework that accurately forecasts microbial abundance trajectories from incomplete longitudinal data, without the need for data imputation

Read more 👉 doi.org/qk8x #OpenAccess

I want to thank the funders, @earlhaminst.bsky.social @quadraminstitute.bsky.social and Anthony, Wing, Kasia, Chris and @cfrioux.bsky.social for help in this project.

cvaNMF is not only useful for microbiomes, but can also be used to discover e.g. 3 signatures describing tumor stages and progression in single cell sequencing data, while identifying key cell types in each.

Several other environments were tested, but to mention soil metagenomes, here we described the "Terrasignatures" that can reliable describe different components of soil. The fine grained nature of allows to reconstruct geographic distances between samples (on 5 Terrasignatures):

In a gut metagenome collection* we re-found a) the original Enterosignatures and b) how these can classify diseases using only 5 enterosignatures

*recommend read: enterotypes from @borklab.bsky.social: doi.org/10.1101/2024...

At it's heart, cvaNMF is a pipeline to ease the computing and k-selection of the NMF method used before. We show that the pipeline can - computationally efficient and in stable API - recover signatures from various datasets and propose a new algorithm to discover the optimal signature number.

Detecting signatures underlying the composition of biological data Abstract. Biological compositional data is inherently multidimensional and therefore difficult to visualize and interpret. To allow for the automatic decom

Led by Anthony Duncan, and after much hard work, we have now published an Enterosignature follow-up paper: cvaNMF

academic.oup.com/nar/article/...
This work represents a generalization of the Enterosignature (ES) framework e.g. discovering ES disease associations, and describe "Terrasignatures"
👇👇👇

YouTube video by Brit With a Mic British Reporter DISMANTLES Trump Bootlicker With ONE Simple Question!

That's a well-prepared journalist, well done: www.youtube.com/watch?v=ufkt...

PhD opportunity at the @quadraminstitute.bsky.social in my group: using population genetics we will explore bacterial evolution in IBD patients in a so far unprecedented spatiotemporal resolution: www.uea.ac.uk/course/phd-d...
Deadline: 6th Jan

PhD opportunity: Exploring the western gut microbiome and how these transfer between family members (2nd Dec 25 deadline).
www.uea.ac.uk/course/phd-d...
This bioinformatic-project will teach high-resolution metagenomics, population genetics, mobile DNA and about bacterial species theory. Please RT

PhD position advertisement that reads "Funded PhD. Exploring the genetics of gut microbiomes spatially resolved in IBD patients. With Professor Falk Hildebrand. Apply by 6 January 2026."

🆕We’re looking for a motivated candidate to explore the evolution of the gut microbiome in patients with Inflammatory Bowel Disease, working on cutting-edge metagenomics with clinical translation 🧬

🗓️ Apply by 6 January 2026
➡️ buff.ly/dFWnLv7

@bioinf.bsky.social

A digital illustration of the gut microbiome with the text "Funded PhD, Evolutionary and Ecological Impact of the Western Lifestyle on the Gut Microbiome, with Dr Falk Hildebrand, Apply by 2 December 2025"

🎓 #PhDPosition !

🍔 Evolutionary and Ecological Impact of the Western Lifestyle on the Gut Microbiome with Dr Falk Hildebrand @bioinf.bsky.social

📅Apply by 2 December

➡️ buff.ly/nZfTKMR

Linking antimicrobial resistance, climate warming, and carbon use efficiency in Arctic soils (HERNANDEZ-GARCIA_UEA_ARIES26) at University of East Anglia on FindAPhD.com PhD Project - Linking antimicrobial resistance, climate warming, and carbon use efficiency in Arctic soils (HERNANDEZ-GARCIA_UEA_ARIES26) at University of East Anglia, listed on FindAPhD.com

PhD opportunity to work in my lab at UEA, together with @drbradbrad.bsky.social and Marc Dumont “Linking AMR, global warming and CUE in deglaciated soils”

www.findaphd.com/phds/project...

Same.

#AlsoTiredOfWaitingForTheEPSTEIN_Files

Interested in modelling metabolism from food -> gut microbiome -> blood ? 5 days left to apply for a fully funded position to investigate this. 👇👇👇

Postdoctoral Research Scientist - Soil Microbiomes

Applications close soon for a postdoctoral researcher to join Dr Falk Hildebrand and Dr Chris Quince at the Earlham Institute, looking at microbial perspectives into land use & climate scenarios.

buff.ly/wR1Ym1z

#SoilHealth #Microbial #SciJobs @bioinf.bsky.social

We want to explore the metabolic interactions among gut bacteria, when the human host eats different foods - maybe this explain partly the Enterosignature structure?
Please do apply for our bioinformatic post to explore this question in metagenomes: jobs.quadram.ac.uk/Details.asp?...

Only 5 days left to apply for our Soil metagenomics position: estimating the impact microbiomes in restored agricultural sites can have on climate change (closing 19th Sep):
jobs.earlham.ac.uk/Details.asp?...

How do you long-read sequence metagenomes? I would argue it starts with the right sample storage & DNA extraction, to enable efficient @nanoporetech.com /@pacbio.bsky.social sequencing, which we investigated in our new paper: www.biorxiv.org/content/10.1...

Massive thanks to Klara for driving this

New project explores potential of soil microbes to achieve UK net zero goals How does different land uses impact soil microbes and their contribution to carbon storage?

Researchers at the Earlham Institute and @quadraminstitute.bsky.social are studying the role of #soil #microbes in carbon storage, and how different land uses impact these communities. 🦠💻🌱🧬

👉 buff.ly/5f1Eo64

@bioinf.bsky.social @tyndallcentre.bsky.social

New project explores potential of soil microbes to achieve UK net zero goals - Quadram Institute Researchers are combining the latest science in climate forecasting and soil science to understand how land use management could enable soil carbon storage

🆕 New project explores potential of soil microbes to achieve UK net zero goals

Providing expertise in cutting edge methodologies for studying microbes, @bioinf.bsky.social and Dr Chris Quince, Group Leaders at the Quadram Institute & Earlham Institute, will together explore key research questions.

An illustration of a network with the text "Metagenomics Research Scientist, to join Falk Hildebrand's group to study the diet impact on the gastrointestinal microbiome. Salary: £37,500 to £42,000, Contract length: 2.5 years, Apply by 30 September 2025"

🆕 Vacancy! We’re looking for a #Metagenomics Research Scientist to join the Laboratory of Dr Falk Hildebrand @bioinf.bsky.social to study diet impact on the gastrointestinal microbiome.

💷 £37,500 - £42,000
🗓️ Apply by 30 September 2025
➡️ buff.ly/uwqGQQm

Last two days to apply for postdoc in my lab, a bioinformatic post to model metabolite fluxes in the gut microbiome during different diets:
jobs.quadram.ac.uk/Details.asp?...

I am seeking a postdoc for my group at UCLA. We work at the intersection of population genetics x microbiome (garud.eeb.ucla.edu). If interested, please message me!

We are on the lookout for postdocs for two different projects at the intersection of ecology, evolution, and the human microbiome.

See thread for more information and reach out!

A vacancy in @bioinf.bsky.social team -2.5 year post on food-associated changes in gut microbiomes.... please see original post for more details

Love that coffee from bluebear

A prebiotic dietary pilot intervention restores faecal metabolites and may be neuroprotective in Parkinson’s Disease - npj Parkinson's Disease npj Parkinson's Disease - A prebiotic dietary pilot intervention restores faecal metabolites and may be neuroprotective in Parkinson’s Disease

(Figure from www.nature.com/articles/s41... as an exemplary analysis target for this post)
@quadraminstitute.bsky.social @earlhaminst.bsky.social

Fig from https://www.nature.com/articles/s41531-025-00885-5

Happy to announce that we have a new 2.5 year post on food-associated changes in gut microbiomes. We are looking for a strong bioinformatician with experience in metagenomics, metabolic modelling, functional genomics, system biology. (application deadline 20.7.25)
quadram.ac.uk/vacancies/me...