Muriel Derrien

Probiotic-mediated modulation of gut microbiome in students exposed to academic stress: a randomized controlled trial - npj Biofilms and Microbiomes npj Biofilms and Microbiomes - Probiotic-mediated modulation of gut microbiome in students exposed to academic stress: a randomized controlled trial

Academia is stressful, maybe fermented milk could keep your gut microbiome in check!

#MicroSky #MicrobiomeSky

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

Bacterial transmission within social groups shapes the underexplored gut microbiome in the lemur Indri indri Abstract. The Indri indri is a critically endangered lemur species that has not successfully been maintained or bred under human care. Investigating this l

🧵 New paper alert!
Our first dive into non-human hosts: the gut microbiome of the critically endangered lemur Indri indri 🐒🌱
Led by talented MSc student Francisca Labisa-Morais!
📄 @isme-microbes.bsky.social
academic.oup.com/ismej/advanc...

Food Microbiome Metabolic Modules (F3M), a tool suite for functional profiling of food microbiomes https://www.biorxiv.org/content/10.1101/2025.07.31.667869v1

Polypeptides synthesized by common bacteria in the human gut improve rodent metabolism - Nature Microbiology Two polypeptides synthesized by common bacterial strains in human gut microbiota lower body fat and blood glucose and increase bone density, improving the metabolism of rodents.

Here the authors propose that gut #microbiota derived peptides exhibit potential for prevention and treatment of human metabolic disorders www.nature.com/articles/s41...

Multimodal AI correlates of glucose spikes in people with normal glucose regulation, pre-diabetes and type 2 diabetes - Nature Medicine Multimodal data from 347 deeply phenotyped individuals including healthy, prediabetic individuals and individuals with T2D report remotely acquired patterns of glucose control via continuous glucose m...

Our @naturemedicine.bsky.social paper on glucose spikes (CGM sensor) and their relationship with physical activity, gut microbiome, genomics, food intake, and sleep via multimodal A.I. Helps identify people with prediabetes who have high risk of progression (cf HbA1c)
www.nature.com/articles/s41...

Dual human milk oligosaccharide-fibre utilisation drives gut microbiome selection during weaning https://www.biorxiv.org/content/10.1101/2025.07.24.666491v1

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

PNGaseA-mediated N-glycan stripping from peptides by infant-derived Bifidobacterium bifidum N-glycans are highly common sources of nutrition for human colonic-dwelling bacteria. These microbes have evolved a several methods to remove N-glycans from proteins; herein we describe the biochemica...

New Pre-print! “PNGaseA-mediated N-glycan stripping from peptides by infant-derived Bifidobacterium bifidum”. This is the first manuscript from the Bifidobacterium and breast milk project🍼🤱👶in collaboration with van Sinderen and Lovering groups
www.biorxiv.org/content/10.1...

Controlled colonization of the human gut with a genetically engineered microbial therapeutic Precision microbiome programming for therapeutic applications is limited by challenges in achieving reproducible colonic colonization. Previously, we created an exclusive niche that we used to engraft...

Engineering the gut microbiome in people with hyperoxaluria to avoid kidney stones
science.org/doi/10.1126/...
@science.org

Milk and mucin glycans orchestrate a synthetic infant gut microbiota structure Dietary and gut glycans drive the composition of an in vitro synthetic community of infant gut microbes.

Another publication in @femsjournals.bsky.social @femsmicro.org 🔬

How do glycans shape the infant gut microbiota? 👶

With a novel in vitro synthetic community we studied the interplay between microbes and HMOs, mucin glycans and GOS/FOS.🍼🤱🦠

#microsky #glycotime

doi.org/10.1093/fems...

Non-antibiotics disrupt colonization resistance against enteropathogens Nature - Non-antibiotic drugs from a wide range of therapeutic classes can alter the ability of gut commensals to resist invasion by enteropathogens, a previously underappreciated side effect of...

Finally online!
Our latest research is out @nature.com: We show that non-antibiotic drugs can disrupt colonization resistance, raising the risk of enteric infections.
rdcu.be/ewwrG

Integrative genomic reconstruction reveals heterogeneity in carbohydrate utilization across human gut bifidobacteria - Nature Microbiology A comprehensive genomic analysis reveals species- and strain-level heterogeneity in carbohydrate utilization potential across bifidobacteria of human origin.

New RESOURCE!

Integrative genomic reconstruction reveals heterogeneity in carbohydrate utilization across human gut bifidobacteria

@arzamasovalex.bsky.social @drlarsbode.bsky.social Andrei Osterman, Jeff Gordon & co

#microbiomesky #microsky

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

Systematic pairwise co-cultures uncover predominant negative interactions among human gut bacteria - Microbiome Background Understanding pairwise bacterial interactions in the human gut is crucial for deciphering the complex networks of bacterial interactions and their contributions to host health. However, the...

Very cool. Here, authors did pairwise co-culturing (mGAM/anaerobiosis) of 97 gut microbial species (113 strains) to infer ecological interactions (n=3233). Most negative were between distant taxa & positive were more among low-abundance taxa.
🔗 microbiomejournal.biomedcentral.com/articles/10....

🚨 Fresh from the press! We created and analyzed over 100 in vitro cyanobacterial consortia using well-characterized model cyanobacterial hosts to better understand how cyanobacteria recruit and interact with their microbiomes.

Check it out: doi.org/10.1093/isme...

GenomeFISH: genome-based fluorescence in situ hybridisation for strain-level visualisation of microbial communities Abstract. Fluorescence in situ hybridisation (FISH) is a powerful tool for visualising the spatial organisation of microbial communities. However, traditio

Very excited to share the first paper out of my Postdoc @CMR:

GenomeFISH: genome-based fluorescence in situ hybridisation for strain-level visualisation of microbial communities.
@sjmcilroy.bsky.social @jamesvolmer.bsky.social @benjwoodcroft.bsky.social

doi.org/10.1093/isme...

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Understanding disease-associated metabolic changes in human colonic epithelial cells using the iColonEpithelium metabolic reconstruction Author summary The human colonic epithelium mediates nutrient absorption and participates in extensive metabolic interactions with the gut microbiota. To better understand the metabolic functions of c...

New paper with the Baloni Lab at Purdue just went online, where we describe the construction of a tissue-specific metabolic model of the colon, iColonEpithelium, compatible with our MICOM platform for simulating microbiota metabolism.

Great work by Boyu Jiang! 👏

journals.plos.org/ploscompbiol...

Exciting Senior Scientist 👩‍🔬 👨‍🔬 role available in my research group 🧠 🦠 - Closing date Tuesday 5th August 2025.

Please Share

@apcmicrobiomeirel.bsky.social @anatneuroucc.bsky.social
Full details here
my.corehr.com/pls/uccrecru...

Multi-omics time-series analysis in microbiome research: a systematic review https://www.biorxiv.org/content/10.1101/2025.07.03.659054v1

@skamrad.bsky.social @kiranrpatil.bsky.social show xenobiotics impact growth of gut bacteria and their metabolic homeostasis by affecting amine metabolism ➡️ www.embopress.org/doi/full/10....

#Editorial

In this month's editorial we reflect on self-reported gender information for corresponding authors and reviewers at Nature Microbiology and identify actions to address disparities. 🧑‍🔬👩‍⚕️👨‍🔬

#GenderEquality #STEM #MicroSky

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

Human gut bacteria bioaccumulate PFAS

Excited to share some key details on our latest research in @natmicrobiol.nature.com reporting intra-cellular accumulation of #PFAS (aka forever chemicals) by certain human gut bacteria. #microsky #mevosky #microbiomesky
www.nature.com/articles/s41...

Our paper demonstrating that within-species warfare interactions are ecologically important on human skin is now published in Nature Micro! www.nature.com/articles/s41...

Guidelines for preventing and reporting contamination in low-biomass microbiome studies Nature Microbiology - In this Consensus Statement, the authors outline strategies for processing, analysing and interpreting low-biomass microbiome samples, and provide recommendations to minimize...

Hope this is useful - consensus statement "Guidelines for preventing and reporting contamination in low-biomass microbiome studies" rdcu.be/er3Io

Guidelines for preventing and reporting contamination in low-biomass microbiome studies - Nature Microbiology In this Consensus Statement, the authors outline strategies for processing, analysing and interpreting low-biomass microbiome samples, and provide recommendations to minimize contaminants.

Guidelines for preventing and reporting contamination in low-biomass microbiome studies www.nature.com/articles/s41... #jcampubs

Really nice paper !

Methanobrevibacter smithii associates with colorectal cancer through trophic control of the cancer bacteriome The human gut is colonized by trillions of microbes that influence the health of their human host. Whereas many bacterial species have now been linked to a variety of different diseases, the involveme...

🚨 New preprint alert!
We report what might be the first mechanistic link between gut Archaea and human disease.
Methanobrevibacter smithii is enriched in CRC patients—and boosts growth of cancer-associated bacteria like F. nucleatum.
www.biorxiv.org/content/10.1...
@archaeasky @microbiomesky

Metabolic ecology of microbiomes: Nutrient competition, host benefits, and community engineering

Review by Erik Bakkeren, Vit Piskovsky, and Kevin R. Foster
www.cell.com/cell-host-mi...

EESMicrobiome

Join us at #EESMicrobiome!

Organisers Mani Arumugam (#uni_copenhagen), Ami Bhatt (@stanfordpress.bsky.social), Peer Bork (@borklab.bsky.social) and Nicola Segata (#CIBIO_UniTrento) look forward to welcoming #microbiome scientists in September at @embl.org!

@events.embl.org

Two-week supplementation of Bifidobacterium adolescentis iVS-1 reduces symptoms associated with lactose intolerance in lactose maldigesters Probiotic supplements containing high β-galactosidase-producing bacteria may aid in the management of lactose intolerance. We previously isolated a strain of Bifidobacterium adolescentis, iVS-1, fr...

Cool study:

Two-week supplementation of Bifidobacterium adolescentis iVS-1 reduces symptoms associated with lactose intolerance in lactose maldigesters www.tandfonline.com/doi/full/10....

📢 Big day for archaeal microbiology!

Today, we jointly shed light on the mysterious world of archaeal extracellular vesicles from human gut archaea - published in @natcomms.nature.com ‬ in parallel with our precious colleagues around @mkrupovic.bsky.social 🇦🇹🤝🇫🇷.