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...

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.

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 🧫

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...

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...

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...

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

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...

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...

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...

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...

💥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... 🧵...

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....

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...

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 👇

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

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...

(1/6) 🌟 Excited to share our new paper! Advancing microbiome safety assessments: opportunities, challenges & recommendations 🧫🦠 This work came out of an academic–industry workshop hosted by @microbiologysociety.org in early 2024. 🔗 www.microbiologyresearch.org/content/jour...

New preprint! Autocycler is a tool for long-read consensus assembly of bacterial genomes. It's like Trycycler but can be run fully automated (without any human intervention). www.biorxiv.org/content/10.1... (1/6)

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]

What happens to microbial genomic evolution in highly stable, closed ecosystems? In this preprint, authors look at 111 MAGs from a Romanian cave isolated from external influences for 5.5My(!) and see more pseudogenisation of core genes & limited HGT. Unsurprising? 🔗 www.biorxiv.org/content/10.1...

Excited to finally share results from my first post-doc @halllab.bsky.social 🫡 E.coli commonly occurs in infant gut microbiota, yet its role during healthy development has been disregarded. In our pre-print, we reveal its fundamental involvement in HMO-degradation. www.biorxiv.org/content/10.1...

It was a memorable experience at #Microbio2025 where I presented my work to colleagues working in the field of microbiology, listened to up-to-date research and had a great time with great people in Liverpool (beautiful city by the way!) 😀 Looking forward to the next one! @microbiologysociety.org

I presented @target-amr.bsky.social at #Microbio25 Please join the network via www.targetamr.org.uk Thanks @lucasbham.bsky.social for the photo.

Excited to share that my first chapter of my #PhD has been published! This was a real labour of love, using qualitative research to set the scene for current #infectiousdisease diagnostic landscapes and how #metagenomics could fit into clinical settings to diagnose infections 🥳 rdcu.be/efTsE

To all enjoying #MicroBio25 remember: all @microbiologysociety.org events rely on our journals - every paper pays 4x travel grants! Make 2025 when you submit a paper to a MicroSoc journal www.microbiologyresearch.org $0 OA for Publish+Read institutions www.microbiologyresearch.org/publish-and-...

Fantastic talk from @raymondkiu.bsky.social on preterm infant gut microbiome in the Knocking Out AMR session this afternoon! Proud to be part of @halllab.bsky.social surrounded by great scientists and research 🧫🧬🥼 #Microbio25 @microbiologysociety.org

Today at 3.35pm IMI's Raymond Kiu @raymondkiu.bsky.social on the Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of preterm infants #microbio25

Find out what my amazing colleagues are working on at #Microbio2025 Luke: poster 263 (Iron transporter in Bifidobacterium) and Charlie: poster 255 (therapeutic Bifidobacterium for IBD). @lukeacton.bsky.social @charliejones17.bsky.social @halllab.bsky.social @imibirmingham.bsky.social

Well deserved Lindsay!! @halllab.bsky.social Amazing public engagement prize lecture at #Microbio2025 from my boss 😀 A role model in science comms #MicrobiomeSky @imibirmingham.bsky.social @microbiologysociety.org

First up at 9am today at #Microbio25 is Prof Lindsay Hall @halllab.bsky.social winner of the Peter Wildy prize, the award recognises excellence in science communication, outreach and engagement in the field of microbiology – congrats Lindsay 🎉

Upcoming talk by @halllab.bsky.social at 4:30pm on early life microbiomes in Room 12! #Microbio2025 #MicrobiomeSky

Highly recommend the on-going #AMGDMarch25 organised by @bacterioskeptic.bsky.social @imibirmingham.bsky.social for anyone who would like to embark on bacterial genomic analyses, this training is a full package: from Bash scripting to using various tools - will be back again next year I believe!

ArgNorm version 0.7.0 released! A lot of improvements, including an update to CARD v4, support for AMRFinderPlus 4, an updated manual curation for many genes argnorm.readthedocs.io/en/latest/wh...

This is my great new preprint with @drvishalcpatel.bsky.social and @halllab.bsky.social. We investigated the gut microbiota in patients with liver disease in which we show an increasing dominance of Enterococcus in the gut of patients with more severe liver disease. www.medrxiv.org/content/10.1...

Really excited that @matthewjdalby.bsky.social is able to share this exciting collaborative study with @drvishalcpatel.bsky.social - its been a long-time coming! We explore how gut #microbiome alterations drive systemic inflammation & immune dysfunction in chronic liver disease (CLD) #LiverDisease

Introducing "Metagenomic Estimation of Dietary Intake", or "MEDI": a data-driven approach to estimating dietary and nutritional intake from stool DNA 💩 - 🍌🥦🐟🥩📈 See @cdiener.com's excellent thread below. We are really proud of this work, and we hope it is useful to the scientific community.