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.

GenomeFetch uses wget ⚙️ in Linux (so won’t work in MacOS unfortunately), pulls metadata automatically 📥, and renames everything by genus/species/strain so your files stay organised and ready to go 🗂️ might be helpful if you’re working with bacterial genomes 👍✨

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

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

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...

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.

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.

Expert opinion

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

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.

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...

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...

🥁 NEW

Our study on infant gut microbiome and #straintransmission is now published in @nature.com:

doi.org/10.1038/s415...

1/10

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...

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...

Massive congratulations!! You truly deserve this!

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...

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.

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 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...

🧵...

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....

This is figure 1 showing general features of infant gut microbiomes.

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 🧪

The ClostPath conferences, which began in 1995, have been a leading venue to bring together top scientists and clinicians studying the molecular biology of clostridia and their role in health and disease. In keeping with this tradition, Clostpath 14 will cover all aspects of clostridia-dependent pathogenesis and will take place September 1 - 4, 2025. The congress will open with a welcome word by Prof. Yasmine Belkaid, President of the Institut Pasteur, followed by an introducing keynote.

🦠 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 🦠🦠🦠

Visual description: graphic depicts Professor Lindsay Hall giving their lecture. Title reads: "Peter Wildly Prize 2025, Interview and Lecture, Lindsay Hall."

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...

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...

#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 👇

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...

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