With sincere appreciation to the @erc.europa.eu, @3domics.bsky.social & HoloRuminant for their support, which enabled this study to come to life.

The 𝟯𝗿𝗱 𝗖𝗼𝗽𝗲𝗻𝗵𝗮𝗴𝗲𝗻 𝗚𝘂𝘁 𝗠𝗶𝗰𝗿𝗼𝗯𝗶𝗼𝗺𝗲 𝗛𝘂𝗯 𝗦𝘆𝗺𝗽𝗼𝘀𝗶𝘂𝗺 was yesterday and 3D’omics was not only there in large numbers, but also received the poster prize! Huge congratulations to Amalia Bogri 🎉🥳 Her fantastic poster impressed the judges and informed the audience about the exciting research we are doing!

Many thanks to the great team at @madeclear.bsky.social for bringing our latest video to life! 💫

3D'omics - Challenges and Solutions YouTube video by 3D'omics

🚨 More news today!

We are excited to share our new video 📽️ presenting the *challenges and solutions* of the last 4 years!
Check it out on youtube!

www.youtube.com/watch?v=RWeq...

Understanding gut microbiomes at this resolution can reshape how we think about:

- Microbial ecology
- Disease mechanisms
- Precision microbiome therapies

We show that spatial structure matters:

- Microbes aren’t randomly distributed
- Distinct niches emerge at tiny scales
- Spatial gradients influence community dynamics

Our method combines advanced spatial sampling with metagenomic sequencing to map microbial communities at the micro-scale.

This allows us to see how microbes are distributed within the gut environment with unprecedented resolution.

The gut microbiome isn’t just “who’s there”; it’s also where ‘they’ are.

Spatial organization influences microbial interactions, host responses, and ecosystem function. But until now, tools for resolving this at the micron scale were limited.

🚨 New preprint alert! 🚨

3D'omics introduces #Micro-scale #spatial #metagenomics — a method to reveal the high-resolution spatial biogeography of gut microbiomes.
🧵👇

www.biorxiv.org/content/10.1...

Did you know that #3Domics had their last in-person meeting last week? We were in beautiful Leuven, discussing the final steps of the project. So good to see so many familiar faces! Excited to share more results soon!

Zooming in on microbial life A pioneering technology that identifies where microbes live and what they do inside the body could change how we understand their role in...

Do you know the EU results packs? They provide excellent summaries of topics, such as "Microbiomes and holobiomes as drivers of a sustainable circular bioeconomy". 🦠

@3domics.bsky.social was featured this month! 🔥 Check it out cordis.europa.eu/article/id/4... (foto credit: Bryan Wang)

Enjoying your summer break? ☀️
@3domics.bsky.social is working hard 👩‍💻 to provide you with exciting 🦠🔬 research once you're back 🏝️.
We are now starting into the hot phase of the last 5 months of the project 🔥🔥🔥
www.3domics.eu

Are you here for the microbes? Listen to this fun podcast!

You might already know our amazing explainer video created by the talented team at @madeclear.bsky.social — if not, check it out here: www.youtube.com/watch?v=Lo75...

We are excited to share that our second video is now in production and launching this summer!

And just like that the #MicrobiomeAtlas course is over. Thank you all for an amazing week and 5 excellent presentations today! #SpatialMicrobiology #3Domics

Another productive day at the #MicrobiomeAtlas course—so much learning and discovery! Can’t wait to hear from the participants tomorrow. Time is just flying by! #3Domics

Today’s bioinformatics session of the #MicrobiomeAtlas course was held with a beautiful view over #Copenhagen 🤩 #3Domics #ScienceWithAView

Day 2 of the #MicrobiomeAtlas course! Yesterday we got to know each other, enjoyed some games and pizza. Today we dove into the labs for hands-on technique learning! Excited for what’s to come! #3Domics #ScienceInAction #LabDay

#Spatial #Microbiomics course starting in one week!

We are so excited to show the world what 3D'omics is working with!

If you are interested & in Copenhagen, consider joining. 2 last-minute spots just opened up!

How growing miniature stomachs can help uncover our evolutionary history with microbes | Microbial Connections How can a microbe responsible for ulcers be either beneficial or harmful to you depending on your genetic background and at what time in life you are infected? And why are fewer Danish children today ...

💡🎧How can a #microbe responsible for #ulcers be either beneficial or harmful? Why are fewer children infected today and what does that mean for our #health? Sandra Breum Andersen gives us the answers in the latest #MicrobialConnections episode👇

microbial-connections.simplecast.com/episodes/how...

Differential effects of synbiotic delivery route (feed, water, combined) in broilers challenged with Salmonella Infantis Salmonella enterica subsp. enterica serovar Infantis (S. Infantis) presents a persistent and multi-drug-resistant threat to poultry production, highli…

📢 Did you see the first OA #publication of 3D'omics yet?!

First author Victoria Drauch & colleagues have published their results on differential effects of synbiotic delivery routes in chicken challenged with Salmonella infections!
Read the full study here!
www.sciencedirect.com/science/arti...

Hi #microbiome community.

If you are interested in microbial networks, feel free to have a look and register in our summer school!

Two days with talks and hands-on on how to annotate your networks and come up with testable hypotheses.
24 and 25 Sep 2025, Leuven , Belgium

@3domics.bsky.social

🧀What do cheese, sourdough, & yogurt have in common? #Microbes!🦠

🎧Listen to postdoc Veronica Sinotte in this episode of our podcast #MicrobialConnections as she explains how #FermentedFood is actually "controlled rot" & how it might have evolved💡
microbial-connections.simplecast.com/episodes/fer...

Interested in #Food #system #innovations and #climate #change?
Attend our seminar "#microbial game-changers": we will be exploring how microorganisms are driving innovation in sustainable food production and climate solutions.

7 April - 9am-4pm - Litteraturhuset i Oslo

www.nmbu.no/en/research/...

*Deadline extended!*

Last chance to join our free workshop on #Spatial #Microbiomics on 12-16 May in #Copenhagen at the Center for Evolutionary Hologenomics. Ideal for PhDs, postdocs & other microbiome enthusiasts.

www.3domics.eu/TrainingEven...

Please share!

Only 4 days left! Register now!

Free workshop on #Spatial #Microbiomics – From Sampling to Analysis"

Join us in May in #Copenhagen at the Center for Evolutionary Hologenomics. Ideal for PhDs, postdocs & other microbiome enthusiasts.

www.3domics.eu/TrainingEven...

Please share!

Deadline approaching! Free workshop on #Spatial #Microbiomics – From Sampling to Analysis"
Join us in May in #Copenhagen at
@hologenomics.bsky.social Ideal for PhDs, postdocs & other microbiome enthusiasts. Register until February 16th: www.3domics.eu/TrainingEven...
Please share!

📢Don't miss out on a great opportunity to join a #free exciting workshop on #Spatial #Microbiomics - From #Sampling to #Analysis in May 2025 here @hologenomics.bsky.social in Copenhagen!🦠

The workshop is arranged by @3domics.bsky.social!
@dg.dk, @holobiontbiology.bsky.social, @hologen.bsky.social

Join us in May in #Copenhagen at @hologenomics.bsky.social
for an exciting #workshop on #microbiomics! "Spatial #Microbiomics – From Sampling to Analysis" 📷May 2025. Ideal for PhDs, postdocs & other microbiome enthusiasts. Register until February 16th: 3domics.eu/TrainingEven... Please re-post!

The learning outcomes focus on gaining an understanding of the differences, challenges, and benefits between micro-scale and conventional microbiomic methods. They also include getting hands-on experience and gaining fundamental expertise to run this workflow.