Yan Shao

We’re grateful to our collaborators @kemriwellcome.bsky.social and across the CHAIN network, all participants and their families, and the editors and reviewers for constructive feedback and guidance throughout.

We hope this resource will inform next-gen probiotic/LBP design: enables geography-informed strain prioritisation, more rigorous engraftment measurement, and synbiotic design by pairing strains with complementary dietary/prebiotic substrates to promote robust, stable engraftment.

Translational outputs: an updated metagenomic workflow plus strain-resolved genetic markers and qPCR assays to improve classification and strain tracking in clinical studies.

We uncovered greatly expanded B. infantis strain diversity and strong biogeographic structure, with predicted metabolic adaptations linked to local dietary substrates.

We resolved long-standing taxonomy/classification confusion with high-resolution phylogenomics, supporting B. infantis and B. longum as distinct species rather than subspecies—crucial for accurate metagenomic epidemiology and downstream functional inference.

Key takeaway is a clear “missing microbe” pattern — B. infantis is common (often dominant) in LMIC infant cohorts across Africa and South Asia, but rare in industrialised and high-income settings in Europe and North America.

Excited to share our latest work on early-life Bifidobacteria. We built a global genomic atlas of 4,000+ genomes from 48 countries for B. infantis and B. longum, expanding previous resources by 15-fold.

Read the press release @sangerinstitute.bsky.social: www.sanger.ac.uk/news_item/mi...

Missing microbes in UK infant gut and probiotics highlighted by global microbiome atlas Experts have created a global atlas of over 4,000 bacterial genomes from two key bacteria found in the infant gut. It highlights one that is often used in infant probiotics is rare in Western babies a...

A global atlas of two key babybiome bacteria has found one of these is missing in UK babies, despite being common in children from other countries.

This atlas is 15x larger than other studies and lays the foundation for more effective, tailored infant probiotics.

www.sanger.ac.uk/news_item/mi...

Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social).

myloasm-docs.github.io

🚨 We’re #hiring a Staff Scientist to drive innovative computational workflows for large-scale, multi-omics data in human microbiome research @sangerinstitute.bsky.social

📅 Closing date: 27th April 2025

📢 Please share & apply!

sanger.wd103.myworkdayjobs.com/en-US/Wellco...

If you have experience in sc/spatial transcriptomics with an interest in microbes....come and join our team as a computational postdoc:
sanger.wd103.myworkdayjobs.com/WellcomeSang...

Incredibly exciting datasets on host-microbe interactions in the lung.

Pls RT and reach out if you are interested.

Really looking forward to attending @microbiologysociety.org annual meeting in Liverpool. As well as a great @pacbio.bsky.social symposium with talks from @jewilki.bsky.social and @yanshao.bsky.social we will have the #Vega system on booth so please stop past for a demo #MicroBio25

Geographical variation in the incidence of colorectal cancer and urinary tract cancer is associated with population exposure to colibactin-producing Escherichia coli Biomedical research has implicated the bacterial metabolite colibactin as a causal risk factor for several cancer types, in particular, colorectal can…

New paper:

We show that population exposure to colibactin producing E. coli lineages ST95 and ST73 largely explains global variation in colorectal cancer incidence. Same STs are also major causes of UTIs and may be similarly involved in urinary tract cancers.

www.sciencedirect.com/science/arti...