Marc-Emmanuel Dumas

Bacteria associated with the cereal leaf beetle act as the insect’s allies in adapting to protease inhibitors, but impair its development in laboratory condition - Scientific Reports Scientific Reports - Bacteria associated with the cereal leaf beetle act as the insect’s allies in adapting to protease inhibitors, but impair its development in laboratory condition

"As HOLOBIONTS, insects are associated with diverse microbiota (Bacteria, Archaea, eucaryotic microorganisms, and viruses) that affect their fitness (positively or negatively)." Sidenote: microbes that do not impact fitness are also part of the holobiont www.nature.com/articles/s41...

Great to see our review on the role of microglia, the 'gardeners' of the brain, in modulating the gut-brain axis make the cover of this months @natrevimmunol.nature.com

University of California faculty push back against Big Brother cybersecurity mandate School officials defend software as bulwark against ransomware, but professors fear potential surveillance of their devices

The journal Science covers the UC spyware saga. The UC administrators’ policy assurances are like saying one does not have to lock one’s car because it is illegal for someone to steal the car or its contents. #highereducation 🧪⚛️🔭 #academicsky www.science.org/content/arti...

A brief guide to statistical analysis of grouped data in preclinical research - Nature Metabolism Clustering and nesting (C&N) arise in many preclinical studies, such as when animals are group-housed or share litters, or in cell culture. Ignoring C&N undermines the validity of analyses. Here, we explain how C&N arise, as well as valid designs and analyses.

#Throwback 🧪

COMMENT | A brief guide to statistical analysis of grouped data in preclinical research

@colbyvorland.bsky.social
L Golzarri-Arroyo
DB Allison

Predicting functions of uncharacterized gene products from microbial communities - Nature Biotechnology FUGAsseM predicts protein function in microbiomes using coexpression patterns from metatranscriptomes and diverse community-wide data.

NEW publication from our lab: One of the first methodologies (FUGAsseM) for gene function prediction from microbial community multi-omics data!

www.nature.com/articles/s41...

🧵⬇️

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A diverse and distinct microbiome inside living trees - Nature Microbiome analyses of living trees show that a single tree can host approximately one trillion bacteria, with microbial communities distinctly partitioned between heartwood and sapwood and with minim...

Trees also have a microbiome 🤓
#microbiology #microbiome
@nature.com
www.nature.com/articles/s41...

The disciplinary matrix of holobiont biology Uniting life’s seen and unseen realms guides a conceptual advance in research

Microbiomes are the foundation of the biosphere. Hosts such as humans, bees, and plants have never been just hosts. They are complex units of biological organization upon which various forces act to shape composition, form, and function. www.science.org/doi/10.1126/...

Methane filtration and metabolic cooperation of microbial communities in cold seep water columns from South China Sea - Communications Biology Metagenomic analysis of cold seep water columns reveals microbial diversity and metabolic interactions driving biogeochemical cycles, emphasizing key roles of methanotrophs and ecological stratificati...

#Methane filtration and metabolic cooperation of microbial communities in cold seep water columns from South China Sea
www.nature.com/articles/s42...

Engineering natural microbial communities: harnessing synthetic communities for bioremediation Microbial bioremediation, a technology using microbial metabolism to degrade or transform environmental pollutants, has garnered significant attention…

Engineering natural microbial communities: harnessing synthetic communities for bioremediation

#CurrOpinMicrobiol from Xihui Xu, Nanjing Agricultural University

www.sciencedirect.com/science/arti...

The mass spectrometry of microbiome-mediated metabolism of food: challenges and opportunities With the exception of molecules acquired through the lungs, skin absorption, or part of a medication regime, nearly all molecules in our bodies origin…

The mass spectrometry of microbiome-mediated metabolism of food: challenges and opportunities

#CurrOpinMicrobiol by @harshagouda.bsky.social et al from @pieterdorrestein.bsky.social

www.sciencedirect.com/science/arti...

Weekly Recap (Aug 2025, part 2): Metagenome assembly from nanopore reads, AI for single-cell analysis, GxE + epistasis in a vertebrate model, estimating GxE for polygenic traits, long-read alignment, agents, nf-core, ... doi.org/10.59350/004... #Rstats #nextflow 🧬🖥️🧪

Personalized Clostridioides difficile colonization risk prediction and probiotic therapy assessment in the human gut Carr et al. show how microbial community-scale metabolic models (MCMMs) predict personalized Clostridioides difficile colonization risk and probiotic efficacy. MCMMs reveal key metabolic strategies ex...

💥Personalized C. difficile colonization risk prediction and probiotic therapy assessment in the human gut💥

I'm very excited about this work, driven by Alex Carr & co-supervised by @cdiener.com

@cp-cellsystems.bsky.social @isbscience.org @nitinbaliga.bsky.social

www.cell.com/cell-systems...

🧵...

The Lancet Countdown on health and plastics Plastics are a grave, growing, and under-recognised danger to human and planetary health. Plastics cause disease and death from infancy to old age and are responsible for health-related economic losse...

The Lancet Countdown on health and plastics - The Lancet www.thelancet.com/journals/lan...

Sir David Nabarro obituary: energetic global health expert Dynamic British physician who helped to spearhead the World Health Organisation’s response to malaria, ebola and Covid-19, dies aged 75

We are deeply saddened by the passing of Professor Sir David Nabarro, Director of @imperial-ighi.bsky.social.

A dynamic British physician, he helped spearhead the @who.int response to #Malaria, #Ebola, and #COVID19.

Find out more about his incredible legacy(£)👇
www.thetimes.com/uk/obituarie...

⏳ Don’t miss it! Submit abstracts & scholarship apps for Microbiome Metabolism & Metabolites by Sept 23 (11:59 PM MT).
📍 Jan 19-22, 2026 | Banff, Canada
👉 keysym.us/KSMicroMetab26
#KSMicroMetab26 #Microbiome #Metabolomics @pieterdorrestein.bsky.social ‪@inesthiele.bsky.social

I am so excited about this meeting. I will cover the discovery of 10,000s new metabolites, including an entirely new class of molecules. Looking forward to hearing and discussing your science on microbiome metabolites and metabolism.

💥 Excited to introduce Bacformer 🦠 - the first foundation model for bacterial genomics. Bacformer represents genomes as sequences of ordered proteins, learning the “grammar” of how genes are arranged, interact and evolve.

Preprint 📝: biorxiv.org/content/10.1...

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Experimental evolution in an era of molecular manipulation - Nature Reviews Genetics In this Review, Ascensao and Desai discuss how methodological advances in genotype and phenotype manipulation are transforming experimental evolution approaches and providing new insights into the und...

Experimental evolution in an era of molecular manipulation www.nature.com/articles/s41... #jcampubs

A Drosophila single-cell 3D spatiotemporal multi-omics atlas unveils panoramic key regulators of cell-type differentiation This work introduces Flysta3D-v2, a 3D spatiotemporal multi-omics database that spans Drosophila development from embryogenesis to metamorphosis. Through the integration of multimodal data, we detail ...

A Drosophila single-cell 3D spatiotemporal multi-omics atlas unveils panoramic key regulators of cell-type differentiation: Cell
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www.cell.com/cell/abstrac...

Does using ChatGPT change your brain activity? Study sparks debate Scientists warn against reading too much into a small experiment generating a lot of buzz.

Does using ChatGPT change your brain activity?

A preprint suggesting that the brains of people writing an essay with ChatGPT are less engaged than are those without any online tools for the task may be generating too much attention given the size of the study…
🧪
www.nature.com/articles/d41...

What does your gut microbiome do? - Help to break down food and its components - Protects your gut from pathogenic bacteria - Help to shape and regulate your immune system - Produce bioactive molecules, like short-chain fatty acids to support your gut cells - Synthesize essential vitamins

The importance of the microbiome by the numbers - 10-100 trillion symbiotic microbial cells in each person - >10,000 different microbe species - The genes in our microbiome outnumber the genes in our genome by about 100 to 1 - Up to 90% of disease can be linked back to the gut microbiome

Happy World Microbiome Day! The Patil Lab at the MRC Toxicology Unit are fascinated by how our microbiome interacts with chemicals in our environment including in food, medicines and pollutants.

Brush up on your knowledge with these great figures made by @rhboston95.bsky.social

Fellowships, grants and career support – Postdoctoral Fellowships – EMBO Supporting internationally mobile postdoctoral researchers in Europe and around the world

Looking for a #LifeSciences postdoctoral #opportunity? 🧪 Have a look at the EMBO Postdoctoral Fellowships for internationally mobile scientists in #Europe and globally.

Apply before 11 July: www.embo.org/funding/fell...
#research #funding #postdoc

Enjoying #metabolomics2025 in Prague! Just presented some of our work on #massspec imaging of #liver fibrosis! @gruevska.bsky.social

Fascinating work on neuropathic pain! Researchers found peripheral nerve injury enhances 4E-BP1-dependent protein synthesis in spinal microglia, pushing them to a reactive state and promoting pain. Excitingly, inhibiting this process reversed pain www.jci.org/articles/vie...

Dietary convergence induces individual responses in faecal microbiome composition Background Dietary variation has been identified as a key contributor to microbiome diversification. However, assessing its true impact in a cross-sectional setting is complicated by biological confou...

📄 New collaborative publication:

"Dietary convergence induces individual responses in faecal microbiome composition"
Astrid Vermeulen et al., now in eGastroenterology.
🔗 egastroenterology.bmj.com/content/3/2/...
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The microbiome for clinicians Preclinical studies suggest a rapidly growing potential for the application of microbiome research in improving patient outcomes. This perspective lays out the potential steps that can be taken toward...

Microbiome for the clinicians | Cell

www.cell.com/cell/fulltex...

Microbial siderophores for One Health One Health is an integrative concept striving for healthy environments, animals, and humans. Microbes play a fundamental role for this concept as they are key drivers of ecosystem stability and host h...

Microbial siderophores for One Health
#Pseudomonas

@cp-trendsmicrobiol.bsky.social Opinion by Zhong Wei et al with @rkmicrobes.bsky.social @veraeva.bsky.social

www.cell.com/trends/micro...

I wouldn't be in the position I'm in now if I hadn't actively sought out and embraced change.

The only issues arise when people don't get that it's possible for a person to excel in more than one specialisation. The term "generalist" seems to be a dirty word in certain academic circles.

An integrative genomic and chemical similarity approach linking fungal secondary metabolites and biosynthetic gene clusters Fungi are well known to biosynthesize structurally complex secondary metabolites (SMs) with diverse bioactivities. These fungal SMs are frequently produced by biosynthetic gene clusters (BGCs). Linkin...

An integrative genomic and chemical similarity approach linking fungal secondary metabolites and biosynthetic gene clusters

bioRxiv from @rokaslab.bsky.social

www.biorxiv.org/content/10.1...

Diet outperforms microbial transplant to drive microbiome recovery in mice - Nature Experiments in mouse models show that proper recovery of the intestinal microbiota following depletion, with or without faecal microbiota transplant therapy, is dependent on syntrophic interactions th...

To restore the gut microbiome after antibiotics, the right diet (rich in carbohydrates, low in fat) was a better approach than fecal microbial transplants (in the experimental model)
www.nature.com/articles/s41...
www.nature.com/articles/d41...