New paper out in Nature Comms 🎉 Congrats to first author @sekid.bsky.social & thanks team & collaborators We show that B. bifidum & E. coli can cooperate in the breastfed infant gut through nutrient cross-feeding, helping shape early-life microbiome development 🦠👶 www.nature.com/articles/s41...

Human milk oligosaccharide mediates mutualism between Escherichia coli and Bifidobacterium bifidum - Nature Communications

Escherichia coli is widespread in healthy breastfed infants, yet its ecological role is unclear. Here, the authors provide insights into the mechanisms supporting its persistence and co-existence with...

nature.com

I have now read this piece and it is very good. Massive respect for @merenbey.bsky.social and Iva for their persistence and documenting this torturous process. Highly recommended reading for anyone who cares about reproducibility in science.

A. Murat Eren (Meren)@merenbey.bsky.social · 4mo ago

How every layer of science's "self-correcting machinery" failed when Iva Veseli and I simply wanted to reproduce the findings of a high-profile study on gut microbiome and autism: merenlab.org/2026/04/15/u...

Here I would like to introduce a genome downloading tool: GenomeFetch 👇🧬 This is a Linux tool written in pure Shell/Bash for downloading bacterial genomes (genome assemblies) from RefSeq or GenBank 🧫

GitHub - raymondkiu/GenomeFetch: GenomeFetch: a fast, user-friendly bacterial genome assembly retrieval tool for RefSeq and GenBank.

GenomeFetch: a fast, user-friendly bacterial genome assembly retrieval tool for RefSeq and GenBank. - raymondkiu/GenomeFetch

github.com

ggCaller v1.5.0 is out! We've removed the integrated clustering to enable users to benefit from new Panaroo features. Now, ggCaller generates GFFs that can be used with any clustering method. But for fans of an integrated ggCaller pangenome workflow read on... github.com/bacpop/ggCal...

GitHub - bacpop/ggCaller: Bifrost graph gene caller.

Bifrost graph gene caller. Contribute to bacpop/ggCaller development by creating an account on GitHub.

github.com

Honoured to have been elected a Fellow of the European Academy of Microbiology @femsmicro.org. This recognition means a lot - and it really reflects the fantastic work of teams and collaborators across the years in advancing early life microbiome research 🤩 fems-microbiology.org/european-aca...

European Academy of Microbiology welcomes 95 new Fellows

Discover the latest election of 95 new Fellows by the European Academy of Microbiology, highlighting diverse expertise in the field.

fems-microbiology.org

Final day (day 5) of #AMGDMar26 at @unibirmingham.bsky.social as @pathogenomenick.bsky.social gave an amazing talk on the applications of bacterial genomics in pandemics.

Research briefings in @nature.com about our latest study of the gut microbiome of infants in nurseries! This work was a true multidisciplinary team effort and a testament to how science can be particularly impactful when built alongside the community. — @livi-ricci.bsky.social and Nicola Segata

Only 2 more days to apply for this post as Research Fellow in the Health Protection Research Unit - Public Health Genomics at the University of Birmingham. Come and join us to exciting, cutting-edge genomics and metagenomics work to deliver public health benefits www.jobs.ac.uk/job/DQE112/r...

Research Fellow at University of Birmingham

Discover Research Fellow jobs and more in higher education on jobs.ac.uk. Apply for further details on the top job board.

jobs.ac.uk

🥁 NEW Our study on infant gut microbiome and #straintransmission is now published in @nature.com: doi.org/10.1038/s415... 1/10

Baby-to-baby strain transmission shapes the developing gut microbiome - Nature

A metagenomic survey of babies attending the first year of nursery detected extensive baby-to-baby microbial strain transmission, pointing to social interactions in infancy as crucial drivers of infan...

doi.org

I am pleased to share that my first postdoc paper from the @halllab.bsky.social is now on bioRxiv! 🎉 We used long-read #metagenomics to explore how the gut microbiome and #antimicrobialresistance landscape shift across advanced chronic #liverdisease (ACLD) www.biorxiv.org/content/10.6...

Decoding the microbiome and resistome of advanced chronic liver disease through long-read metagenomics

Introduction - Patients with advanced chronic liver disease (ACLD) and underlying cirrhosis frequently require repeated courses of antimicrobial therapy, with both the frequency and spectrum of antimi...

biorxiv.org

Have research, results, or ideas to share with the microbial ecology community? Don’t miss your chance to present it at #MMEG2025 - abstract submissions close 2 November! 📨 Submit your abstract: appliedmicrobiology.org/ems-event-ca...

It’s been a bit over 2 months since the main results of my PhD work on reconstructing carbohydrate utilization pathways in human bifidobacteria were finally published; so I guess it’s a good time to update the previous thread (1/7) www.nature.com/articles/s41...

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.

nature.com

Alex Arzamasov@arzamasovalex.bsky.social · 2y ago

Happy to share a preprint with the results of my PhD work on creating a comprehensive genomic encyclopedia of carbohydrate metabolism in human-colonizing bifidobacteria. TL;DR: there's tons of variability. A thread with results (1/) www.biorxiv.org/content/10.1...

Sometimes you meet absolutely incredible bioinfo-magicians. It was a huge privilege when @shenwei356.bsky.social joined our group for a year on an @embl.org sabbatical. While here, he developed a new way of aligning to millions of bacteria, called LexicMap 1/n www.nature.com/articles/s41...

Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology

LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.

nature.com

Wonderful plenary lecture by Prof Dena Lyras to kick off Clostpath 2025 in Paris! @pasteuredu.bsky.social @monashuniversity.bsky.social #clostpath14

Really pleased to see this study led by @raymondkiu.bsky.social now published in @natcomms.nature.com! We show that probiotics help modulate the preterm infant 👶#microbiome - to reduce ARGs, lower MDR bacteria 🦠 & increase beneficial Bifido ✨ Huge team effort! www.nature.com/articles/s41...

Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants - Nature Communications

Here, the authors show that giving probiotics to very low birth weight preterm babies can help reduce harmful antibiotic-resistant bacteria in the gut and support the development of a healthier microb...

nature.com

Hall Lab @halllab.bsky.social · 2y ago

So excited to see this preprint out! Huge congrats to @raymondkiu.bsky.social on bringing this preterm microbiome study together with some really neat well-controlled clinical subgroups & analysis. As always we couldn't do this without amazing team members & collaborators! Check out details below 👇

💥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... 🧵...

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...

cell.com

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....

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...

microbiomejournal.biomedcentral.com

Around 25% of U.S. infants lack detectable Bifidobacterium, regardless of birth or feeding method. This deficit could have implications for immune health and the trajectory of noncommunicable diseases, according to a study published in Communications Biology. go.nature.com/4lgA1ls 🧪

🦠 ClostPath 2025 is coming to Paris! 🇫🇷 Join us Sept 1-4, 2025 at Institut Pasteur for the 14th International Conference on Molecular Biology & Pathogenesis of Clostridia. 📝 Register now: www.clostpath2025.conferences-pasteur.org/home

Day 4 of IMI Summer school started with Feeding the Future and green bread 🍞 with UoB's Dr Helen Onyeaka, GI infections with Dr Ella Rodwell and Exploring the World of Gut Bacteria with the fabulous @halllab.bsky.social 🦠🦠🦠

Peter Wildy Prize Lecture and Interview with Prof. Lindsay Hall from Annual Conference 2025 is now available on YouTube. Watch the full interview and lecture: 'Guardians of the Gut Bringing Microbiome Science to Life through Public Engagement' microb.io/40s1zvB #Microbio25

Half way through the IMI Summer school 2025 starts with a fantastic Q&A panel with our own UoB students and Postdocs and @wvschaik.bsky.social giving a great talk on AMR & Phages 🦠🦠

How does your diet impact the microbiome? Let's find out...🦠🦠

Culture club! Do probiotic yoghurt drinks really contain live bacteria? Let's find out at IMI Summer school 2025 🦠🦠

🌍 #WorldMicrobiomeDay 2025 At @halllab.bsky.social we’re uncovering how microbes - right from day one - help shape the gut, strengthen immunity, and protect against infection. We're exploring how, when, and which microbes colonise - in order to develop interventions for a healthier start to life.

Newly published study by Prof Lindsay Hall @halllab.bsky.social and Prof Willem van Schaik @wvschaik.bsky.social finding that antibiotic resistant Staphylococcus haemolyticus bacteria are common in premature babies www.birmingham.ac.uk/news/2025/wi...

#NatMicroPicks Tracking the gut microbiome evolution 🦠 A big data analysis of gut microbiome of kids from infancy to 8 years of age. #MicroSky #MicrobiomeSky www.nature.com/articles/s41...

Gut microbiome evolution from infancy to 8 years of age - Nature Medicine

In a unique cohort of twins followed from birth to 8 years of age, shotgun sequencing of stool samples reveals that the transmission, persistence and evolutionary adaptation of bacterial strains are s...

nature.com

Amazing to see this now published! Congrats to @lisalamberte.bsky.social and @wvschaik.bsky.social - on leading this important #microbiome study on #AMR and Staphylococcus haemolyticus in the preterm gut 👇

Willem van Schaik@wvschaik.bsky.social · last yr.

I am delighted that our manuscript 'Staphylococcus haemolyticus is a reservoir of antibiotic resistance genes in the preterm infant gut' is now published. www.tandfonline.com/doi/full/10.... Big thank you to all co-authors, particularly @lisalamberte.bsky.social and @halllab.bsky.social

I am delighted that our manuscript 'Staphylococcus haemolyticus is a reservoir of antibiotic resistance genes in the preterm infant gut' is now published. www.tandfonline.com/doi/full/10.... Big thank you to all co-authors, particularly @lisalamberte.bsky.social and @halllab.bsky.social

Staphylococcus haemolyticus is a reservoir of antibiotic resistance genes in the preterm infant gut

Staphylococcus haemolyticus is an important cause of sepsis in preterm infants, with gut colonization being recognized as a risk factor for infection. To better understand the diversity of S. haemo...

tandfonline.com

An exciting new Doctoral Training Programme in Microbial Genomics for Health Protection, in collaboration with the UK Health Security Agency @ukhsa.bsky.social, has just launched, funded by @nihr.bsky.social there are 9 PhD projects available (UK students only) www.birmingham.ac.uk/research/cen...

PhD Microbial Genomics for Health Protection, Biosciences - University of Birmingham

PhD in Microbial Genomics, exciting new Doctoral Training Programme in Microbial Genomics for Health Protection in collaboration with the UK Health Security Agency (UKHSA) launches

birmingham.ac.uk