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Reposted by Raymond Kiu

Applied Microbiology International @amiposts.bsky.social · 7d

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...

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Alex Arzamasov @arzamasovalex.bsky.social · 21d

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...

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Zamin Iqbal @zaminiqbal.bsky.social · Sep 10

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.

www.nature.com

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Raymond Kiu @raymondkiu.bsky.social · Sep 1

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

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Hall Lab @halllab.bsky.social · Aug 17

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...

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Sean Gibbons 🦠💩 @gibbological.bsky.social · Aug 6

💥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...

www.cell.com

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Guillaume Méric @gmeric.bsky.social · Jul 16

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

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Nature Portfolio @natureportfolio.nature.com · Jul 14

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 🧪

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

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Institut Pasteur | 130 years of biomedical research @pasteur.fr · Jul 11

🦠 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

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.

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Institute of Microbiology and Infection @imibirmingham.bsky.social · Jul 3

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 🦠🦠🦠

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Microbiology Society @microbiologysociety.org · Jul 3

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

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

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Institute of Microbiology and Infection @imibirmingham.bsky.social · Jul 2

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 🦠🦠

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Institute of Microbiology and Infection @imibirmingham.bsky.social · Jul 2

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

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Institute of Microbiology and Infection @imibirmingham.bsky.social · Jul 1

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

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Hall Lab @halllab.bsky.social · Jun 27

🌍 #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.

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Institute of Microbiology and Infection @imibirmingham.bsky.social · Jun 30

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...

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Nature Microbiology @natmicrobiol.nature.com · Jun 26

#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...

www.nature.com

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Hall Lab @halllab.bsky.social · Jun 23

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 · Jun 23

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...

www.tandfonline.com

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Willem van Schaik @wvschaik.bsky.social · Jun 23

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...

www.tandfonline.com

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Reposted by Raymond Kiu

Institute of Microbiology and Infection @imibirmingham.bsky.social · May 23

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

www.birmingham.ac.uk

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Hall Lab @halllab.bsky.social · May 27

(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...

Assessing the safety of microbiome perturbations

Everyday actions such as eating, tooth brushing or applying cosmetics inherently modulate our microbiome. Advances in sequencing technologies now facilitate detailed microbial profiling, driving inten...

www.microbiologyresearch.org

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Ryan Wick @rrwick.bsky.social · May 21

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)

Autocycler: long-read consensus assembly for bacterial genomes

Motivation Long-read sequencing enables complete bacterial genome assemblies, but individual assemblers are imperfect and often produce sequence-level and structural errors. Consensus assembly using T...

www.biorxiv.org

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Tami Lieberman @contaminatedsci.bsky.social · May 1

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]

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Guillaume Méric @gmeric.bsky.social · Apr 11

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...

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David Seki @sekid.bsky.social · Apr 9

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...

www.biorxiv.org

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