Segata Lab

IBFG slide

We're happy to welcome @nmquijada.bsky.social to our lab as a visiting researcher!

Narciso is a researcher from Instituto de Biología Funcional y Genómica (IBFG) who investigates food microbiome and resistome as well as contributes to bioinformatics efforts in the field github.com/nmquijada

FEMS2025

Our lab member @amirn.bsky.social will be attending the @femsmicro.org conference in Milan 🇮🇹 next week.

Feel free to connect or meet up at the #FEMS2025!

If you miss the talk on Wednesday (details ⬇️)
you can check out the poster with ID Number: wed_2.1_519_S

FEMS2025

Our lab member @amirn.bsky.social will be attending the @femsmicro.org conference in Milan 🇮🇹 next week.

Feel free to connect or meet up at the #FEMS2025!

If you miss the talk on Wednesday (details ⬇️)
you can check out the poster with ID Number: wed_2.1_519_S

Highly recommended!

🧬🖥️ Postdoc positions available SOON!!
Looking for researchers with strong computational skills (programming essential) to work on microbiome & phylogenetics projects.
📅 Start on Nov 1, 2025 (flexible)
📍 Trento, Italy
DM me for details or share!
#postdocjobs #microbiome #metagenomics #phylogenetics

Francesco is building a team 🥁

He is an open minded researcher with expertise in human microbiome and bioinformatics.

Plus I am pretty sure you will enjoy chatting with him about future projects and your potential contribution!!

A Step-by-Step Guide to Publishing a BugSigDB Study
by @toriaburah.bsky.social

#outreachy @bioconductor.bsky.social

burah.hashnode.dev/step-by-step...

We're happy to welcome Karlijn Johanna Van Dijk to our lab as a visiting researcher!

Karlijn is a PhD student from #UniversityofStavanger who investigates human gut microbiome in oncology.

www.uis.no/en/profile/4...

📥 You have only until 24 June to submit your abstract for 'The human microbiome'❗

🔬💊 Explore cutting-edge breakthroughs in #microbiome research, from methodological innovations to integrative approaches and personalised therapeutics. Join #EESMicrobiome 🦠🔍

➡️ https://s.embl.org/ees25-08-bl

MetaPhlAn 4.2.2 release (initial long-read sequencing support and database update) Announcement We are pleased to share that MetaPhlAn 4.2.2 is now available, which incorporates taxonomic profiling of long-read metagenomes for the first time and includes a new version of the MetaPhl...

The new version of MetaPhlAn v4.2.2 released!

📌taxonomic profiling of long-read metagenomes for the first time
📌new version of the MetaPhlAn db (vJan25_202503) containing >21k new SGBs

Try it out & @hutlab.bsky.social and we are looking forward to your feedback!
forum.biobakery.org/t/metaphlan-...

Very excited to see the long-read #microbiome profiling feature included in this tool! I'll be taking a look at #PacBio HiFi performance in the near future.

MetaPhlAn 4.2.2 release (initial long-read sequencing support and database update) Announcement We are pleased to share that MetaPhlAn 4.2.2 is now available, which incorporates taxonomic profiling of long-read metagenomes for the first time and includes a new version of the MetaPhl...

The new version of MetaPhlAn v4.2.2 released!

📌taxonomic profiling of long-read metagenomes for the first time
📌new version of the MetaPhlAn db (vJan25_202503) containing >21k new SGBs

Try it out & @hutlab.bsky.social and we are looking forward to your feedback!
forum.biobakery.org/t/metaphlan-...

Today I went to my daughter’s childcare to talk to the toddlers about heart health and gut microbes ❤️

They were very excited to tell me about their fav fruits and veggies

Big thanks to @cibiocm.bsky.social for the toy microbes 🦠🙏

@monashuniversity.bsky.social

EESMicrobiome

Join us at #EESMicrobiome!

Organisers Mani Arumugam (#uni_copenhagen), Ami Bhatt (@stanfordpress.bsky.social), Peer Bork (@borklab.bsky.social) and Nicola Segata (#CIBIO_UniTrento) look forward to welcoming #microbiome scientists in September at @embl.org!

@events.embl.org

Shotgun Metagenomics Identifies in a Cross‐Sectional Setting Improved Plaque Microbiome Biomarkers for Peri‐Implant Diseases Aim This observational study aimed to verify and improve the predictive value of plaque microbiome of patients with dental implant for peri-implant diseases. Materials and Methods Patients were in.....

In this study just published at the Journal of Clinical Periodontology - a collaboration between @cibiocm.bsky.social and PreBiomics - we evaluated the microbiome of dental implants using metagenomic sequencing

onlinelibrary.wiley.com/doi/10.1111/...

EESMicrobiome

Join us at #EESMicrobiome!

Organisers Mani Arumugam (#uni_copenhagen), Ami Bhatt (@stanfordpress.bsky.social), Peer Bork (@borklab.bsky.social) and Nicola Segata (#CIBIO_UniTrento) look forward to welcoming #microbiome scientists in September at @embl.org!

@events.embl.org

🥁NEW: our latest collaboration with PreBiomics on plaque microbiome is OUT!

This manuscript was the winner of the third 2025 Jaccard - EFP Prize in Periodontology.

Check out 🧵⬇️

🥁NEW: our latest collaboration with PreBiomics on plaque microbiome is OUT!

This manuscript was the winner of the third 2025 Jaccard - EFP Prize in Periodontology.

Check out 🧵⬇️

Description of Catenibacterium mitsuokai subsp. tridentinum subsp. nov., an anaerobic bacterium isolated from human faeces, and emended description of C. mitsuokai A recent metagenomic survey has revealed an unknown bacterial clade within the Catenibacterium mitsuokai species to be significantly more prevalent in non-urbanized populations, compared to urbanized ...

Let us introduce a new subspecies:

✨Catenibacterium mitsuokai subsp. tridentinum✨

Plus, we also propose a taxonomic reclassification of publicly available reference genomes belonging to the C. mitsuokai sp.

More details ⬇️
www.microbiologyresearch.org/content/jour...

Roberta Marconi at #GutMicrobiology2025!

Yesterday at #GutMicrobiology2025!

newspapers

In the 🗞️🇮🇹

Description of Catenibacterium mitsuokai subsp. tridentinum subsp. nov., an anaerobic bacterium isolated from human faeces, and emended description of C. mitsuokai A recent metagenomic survey has revealed an unknown bacterial clade within the Catenibacterium mitsuokai species to be significantly more prevalent in non-urbanized populations, compared to urbanized ...

Let us introduce a new subspecies:

✨Catenibacterium mitsuokai subsp. tridentinum✨

Plus, we also propose a taxonomic reclassification of publicly available reference genomes belonging to the C. mitsuokai sp.

More details ⬇️
www.microbiologyresearch.org/content/jour...

Pooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer - Nature Medicine An analysis of 18 metagenomic datasets of individuals with colorectal cancer, adenomas and healthy controls yields improved cancer prediction accuracy based solely on gut metagenomics, as well as the ...

🥁NEW publication from our lab:
the largest meta-analysis of gut microbiome associations with CRC!

www.nature.com/articles/s41...

🧵⬇️

1/6

In summary, our study represents the largest meta-analysis of gut microbiome associations with CRC.

This study was led by Gianmarco Piccinno and we would like to thank @cibiocm.bsky.social members, the ONCOBIOME Consortium and the PROSPECT team for this great collaboration.

6/6

fig6

We also investigated the within species differential gene carriage and strain-differentiation between controls and CRC.

www.nature.com/articles/s41...
www.nature.com/articles/s41...

5/6

Fig3

We studied the gut microbiome composition along stages of CRC and primary tumor location.

www.nature.com/articles/s41...

4/6

Fig2

We exploited machine learning and meta-analysis approaches to characterize the association of the gut microbes with CRC.

The gut microbiome signature is characterized by peculiar species which are very unlikely inhabitants of the healthy gut!

www.nature.com/articles/s41...

3/6

fig1

We leveraged >3,700 fecal samples derived from healthy, adenoma and CRC individuals and sequenced with shotgun metagenomics.

www.nature.com/articles/s41...

2/6

Pooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer - Nature Medicine An analysis of 18 metagenomic datasets of individuals with colorectal cancer, adenomas and healthy controls yields improved cancer prediction accuracy based solely on gut metagenomics, as well as the ...

🥁NEW publication from our lab:
the largest meta-analysis of gut microbiome associations with CRC!

www.nature.com/articles/s41...

🧵⬇️

1/6

. @marconiroberta.bsky.social is attending and presenting at the upcoming GUT MICROBIOLOGY SYMPOSIUM gutmicrobiology-2025.symposium.inrae.fr

Her talk is about our latest cultivation efforts. It will be on Tuesday at 17:15.

Come say HI and discuss ☕️ and gut microbiome with Roberta!