Come and meet us at #EESMicrobiome in Heidelberg! We are excited to share our research with you 🥳

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Interested in how it all began? Check out our paper about the Estonian Microbiome Cohort! ➡️ www.nature.com/articles/s41...

The entire archive of CDC datasets can be found here.

HUGE shoutout to data archivists- this work is important 👏🙌🏻

archive.org/details/2025...

Thank you to organizers of the Research Days of Institute of Biomedicine and Translational Medicine for inviting me to present our project on type 2 diabetes medications and the gut microbiome. I really appreciate the feedback and questions. Find out more from the preprint: doi.org/10.1101/2024...

Early life microbial succession in the gut follows common patterns in humans across the globe Nature Communications - Here, the authors perform a global analysis of over 3000 infant gut samples revealing a universal pattern of microbial changes over the first 1.5 years, with declines in...

Super proud of this paper on infant gut microbiome age coming from my lab. The paper has just been published with @springernature.bsky.social in @naturecomms.bsky.social. Read about it here: rdcu.be/d6cCw.

A framework for understanding collective microbiome metabolism - Nature Microbiology This Perspective explores why microbiome members perform partial metabolism of substrates and suggests that proteome efficiency is a driver of collective microbiome metabolism.

Thrilled to announce that Matthias Hülsmann's new perspective is now out in @naturemicrobiol.bsky.social! This exciting work is shaping how our group thinks about collective microbiome metabolism. Check it out! www.nature.com/articles/s41...

Spatially restricted immune and microbiota-driven adaptation of the gut - Nature Intestinal regionalization is characterized by robust and resilient structural cell states and the intestine can adapt to environmental stress in a spatially controlled manner through crosstalk betwee...

1/ Keen to share the story of my postdoc research out in @natureportfolio.bsky.social! We built a massive resource characterizing the spatial landscape of the gut—and yes, we dug deep into the biology too. If you’ve got a minute, let me walk you through the story. 🧵👇
www.nature.com/articles/s41...

The microbiome in cancer The gut microbiome plays a crucial role in cancer development and progression, by influencing the host immune system and metabolism.

More #NatureReviewsCancer updates 🚨

We recently launched a collection on the #microbiome in cancer. While its role is still debated, the collection presents a selection of articles from #SpringerNature journals to highlight our current understandings.🧫🦠

😀👉 bit.ly/48u8WFH

Your friends shape your microbiome — and so do their friends Nature - Analysis of nearly 2,000 people living in remote villages in Honduras reveals who’s spreading gut microorganisms to whom.

Your friends shape your microbiome — and so do their friends

Analysis of nearly 2,000 people living in remote villages in Honduras reveals who’s spreading gut microorganisms to whom.

www.nature.com/artic...


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Results 10 yrs metagenomic sequencing for CNS infections www.nature.com/articles/s41...

Impressive.

Key take homes for me.
1) Time to result still long - addressable but a barrier currently.
2) 10% contamination.
3) Despite using cutting edge tests a "causative" organism found in only 15%.

Targeted protein evolution in the gut microbiome by diversity-generating retroelements
www.biorxiv.org/content/10.1...

Nice paper on diversity generating retroelements in the Bacteroides:

The mOTUs online database provides web-accessible genomic context to taxonomic profiling of microbial communities Abstract. Determining the taxonomic composition (taxonomic profiling) is a fundamental task in studying environmental and host-associated microbial communi

Reading: academic.oup.com/nar/advance-...

The mOTUs online database provides web-accessible genomic context to taxonomic profiling of microbial communities

Spatiotemporal dynamics during niche remodeling by super-colonizing microbiota in the mammalian gut Fecal microbiota transplantation (FMT) therapies hold promise but suffer from variable transplantation efficiencies. Here, we examine microbiome spatiotemporal dynamics post-FMT with a super-colonizin...

New paper from the lab out in Cell Systems. “Spatiotemporal dynamics during niche remodeling by super-colonizing microbiota in the mammalian gut”
www.cell.com/cell-systems...

Estimates of microbiome heritability across hosts - Nature Microbiology In this Perspective, Morris and Bohannan discuss heritability of microbiome-mediated traits across hosts and future research questions with implications for animal and plant breeding.

Estimates of microbiome heritability across hosts.
#Microbiome #NatureMicrobiology #BioSky #SciSky 🧪
www.nature.com/articles/s41...

Hi, Jan! I would love to be added there. Thank you!

Incredible graphic - the myriad of ways that bacteria defend themselves against antibiotics.

14 resistance mechanisms, summarised by Idan Yelin & Roy Kishony in Cell

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

Hot off the press: "Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations" www.sciencedirect.com/science/arti...

See below for @suguru-nishijima.bsky.social 's thread on the preprint!

#microsky #microbiome

Excited to share our latest preprint on a novel computational tool to predict fecal microbial load solely from relative species profiles! Our study revealed that fecal microbial load is a substantial confounder in microbiome-disease association studies.
www.biorxiv.org/content/10.1...

Bluesky, I want to share with you one of my favourite papers:

After editing, this very short letter to New Scientist is even shorter now. But I think it gets the point across! @faecalmatters.bsky.social

Your hitchhiker's guide to microbiome studies:
journals.asm.org/doi/epub/10....

Pseudomonas aeruginosa faces a fitness trade-off between mucosal colonization and antibiotic tolerance during airway infection - Nature Microbiology Tn-seq and live imaging of Pseudomonas aeruginosa during airway epithelial organoid infections reveal metabolic adaptations and trade-offs between growth and antibiotic tolerance in biofilm lifestyle,...

I'm new here, so I'll share our recent work here too 😁🧫

Using Tn-seq + live imaging in engineered airway organoids, we explored the fitness tradeoffs P. aeruginosa faces while growing and surviving antibiotic treatment on the mucosal surface.

Check it out: www.nature.com/articles/s41...

#MicroSky

Welcome all (new) followers! Besides our work on probes & biosensors I'd like to share what I know about #Rstats and #DataViz. So I composed a book on data visualization with R & ggplot2 (it's work in progress).
Target audience = wet lab scientists.
Link: joachimgoedhart.github.io/DataViz-prot...

[looking at Bluesky over the past 2 days] So this is what the Cambrian explosion must have felt like

Human xenobiotic metabolism proteins have full-length and split homologs in the gut microbiome https://www.biorxiv.org/content/10.1101/2024.11.06.622278v1 Xenobiotics, including pharmaceutical drugs, can be metabolized by both host and microbiota, in some

Human xenobiotic metabolism proteins have full-length and split homologs in the gut microbiome www.biorxiv.org/content/10.1101/2024.11....

Hello, Bluesky! I'm Annabel, a PhD student in the Tartu Microbiome group led by Prof. Elin Org at the University of Tartu (EE).

I am interested in the long-term effects of medications on the gut microbiome and early-life microbiome development.

I also like photography, sci-fi, and crocheting 🌿