Precisely calling mutations across hundreds of bacterial isolates has been hard, requiring manual filtering and expertise. Until now, using AccuSNV. Herui Liao trained an ML model based on our previous meticulously called SNVs. www.biorxiv.org/content/10.1...

This week @science.org Dual #transposon sequencing profiles the #genetic interaction landscape in #bacteria | Science www.science.org/doi/10.1126/... 🦠🔬🧫🧬

our software, microbetag, for the annotation of microbial co-occurrence networks with phenotypic traits & metabolic complementarities was just published A Cytoscape app is also available to make your life easier (and prettier) #microbiome #metabolic-modeling #networks

My commentary article, featuring the work of Aasmets et al. on the long-lasting effects of medications on the gut microbiome, is now out in mSystems @asm.org #microbiome #microsky doi.org/10.1128/msys...

How much of selection in human microbiomes is driven by phage? Excited to share our latest, led by A. Delphine Tripp, showing a case where phage is just not that important: Phage-mediated lysis does not determine Cutibacterium acnes colonization on human skin www.biorxiv.org/content/10.1... 🧵

New online! Fusobacterium nucleatum: ecology, pathogenesis and clinical implications

If you missed Dr Chudan Xu's talk on what happens when we don't eat enough fibre, the preprint is now live 👇 www.medrxiv.org/content/10.1... #EESMicrobiome @events.embl.org

Starting my journey from Australia to Heidelberg 🇩🇪 to the @embl.org Human Microbiome conference It’s not every day we get the chance of 4 days of human microbiome research 🤩🤩🤩 I’m so excited Still chance to attend it online 👇 www.embl.org/about/info/c...

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?...

Dissecting microbial communities with single-cell transcriptome analysis www.science.org/doi/abs/10.1... #jcampubs

Exams = stress. 📚 Our new study shows that a probiotic strain (L. rhamnosus CNCM I-3690) modulated the gut microbiome during academic stress, with ties to lower anxiety. 🔗 Vázquez-Castellanos et al. doi.org/10.1038/s415...

Started off as a reading group and led to a nice mini-review of microbiome evolution in natural communities. Complete credit to Abby for leading this fun collab! #mevosky Investigating bacterial evolution in nature with metagenomics doi.org/10.1016/j.mi...

This first-author publication is my… first! Archaea kill bacteria by targeting their Achilles’ heel: peptidoglycan. Big shoutout to @ahocher.bsky.social‬, @valeriesoo.bsky.social‬, Pauline Misson, @tobiaswarnecke.bsky.social‬ and MRC LMS Proteomics. A thread 🔽 journals.plos.org/plosbiology/...

Academia is stressful, maybe fermented milk could keep your gut microbiome in check! #MicroSky #MicrobiomeSky www.nature.com/articles/s41...

🧵 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

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

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 www.nature.com/articles/s41... #jcampubs

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...

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

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...

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

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...

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...

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... 🧵1/7

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...

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...

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 www.nature.com/articles/s41... #jcampubs

🚨 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...

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

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 🇦🇹🤝🇫🇷.

Scientists identified a novel indole-3-propionate producer, Enterocloster aldenensis, which produced this key metabolite exclusively from indole-3-lactate These findings open new avenues for treatments in diseases with an altered tryptophan metabolism: www.tandfonline.com/doi/full/10....

🧵5 Top Free Alternatives to BioRender for Scientific Illustrations! These five websites offer free scientific illustrations for biologists. Great for presentations, research papers and other research communication needs. Save and share the post!

📽️If you missed the special #MVIF event "The Role of the Nagoya Protocol in Protecting Microbial Diversity Through Fair Use," recordings are now available on @cassyni.bsky.social and YouTube! Thanks to our wonderful speakers for their highly informative talks filled with valuable tips!🌷

A GO for studying the microbiology of the human #Microbiome! Congrats @tclavel.bsky.social, Tom’s team and collaborators. www.nature.com/articles/s41...

There's still time to register for #MVIF today! **Special event on The role of the Nagoya Protocol in protecting microbial diversity through fair use** cassyni.com/s/mvif-39

Thrilled to share this collaborative work by Kristie Yu, Francis Chandra, Amina Schartup and teams @Scripps_Ocean and @UCLA showing that an engineered gut bacterium can be used to reduce the neurotoxic effects of dietary methylmercury www.cell.com/cell-host-mi...

Do people in the same household share strains when they have the same species? How many cells transmit when a strain is shared? Can strain composition be dynamic when species composition is stable? We answer these and related questions for the facial skin microbiome in our latest paper. 🧵[1/10]

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...