Segata Lab

Segata Lab

@cibiocm.bsky.social

The Laboratory of Computational Metagenomics led by Nicola Segata **We are hiring, get in touch if interested!** http://segatalab.cibio.unitn.it/ Moderator @svetlanaup.bsky.social

2.3K followers703 following314 posts

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Segata Lab
@cibiocm.bsky.social

🎉 Exciting news from our lab! cFMDv1.3.2 is now live. This release marks a significant expansion of cFMD: 📊 681 newly integrated food metagenomes from 22 public datasets 18,180 total MAGs across 4,125 metagenomes 54 countries (now including 🇲🇦) 100+ food-related studies 1/3

Segata Lab reposted

Microbiome Virtual International Forum
@microbiomevif.bsky.social

🚀 A new #MVIFconversations episode drops this Monday, stay tuned! Until then, catch up on Episode 7 with @elisabethbik.bsky.social and get ready! #podcast #microbiome #science

Microbiome Virtual International Forum@microbiomevif.bsky.social

#MVIFconversations podcast episode 7 with @elisabethbik.bsky.social is OUT! ▶️ Spotify: open.spotify.com/episode/5YcW... ▶️ Amazon music: music.amazon.com/podcasts/81c... ▶️ Apple Music: podcasts.apple.com/us/podcast/e... ▶️ YouTube podcast: youtu.be/7-4QeEz2fyc?... 1/2

open.spotify.comopen.spotify.com

Segata Lab reposted

Matt Olm
@mattolm.bsky.social

Introducing Microbiome Repo, a catalog of every public human gut metagenome (>500k samples) with metadata pulled straight from sequence archives, papers, and supplements! olmlab.github.io/microbiome_r... Published gut metagenomes? Search your name and see if it got your study! Feedback welcome

olmlab.github.ioMicrobiome RepoMicrobiome Repo: every public human shotgun-metagenome study (registry) and a curated, evidence-linked catalog of human gut metagenomes of all ages with per-sample metadata.

Segata Lab reposted

APC Microbiome Ireland
@apcmicrobiomeirel.bsky.social

𝐒𝐞𝐬𝐬𝐢𝐨𝐧 𝟐 The 2026 𝐶ℎ𝑎𝑟𝑙𝑒𝑠 𝐷𝑜𝑛𝑜𝑣𝑎𝑛 𝑀𝑖𝑐𝑟𝑜𝑏𝑖𝑜𝑚𝑒 𝐴𝑤𝑎𝑟𝑑 has been presented to Professor Nicola Segata - Laboratory of Computational Metagenomics @cibiocm.bsky.social. He presented his work for the Distinguished international APC lecture: “𝐴𝑐𝑞𝑢𝑖𝑠𝑖𝑡𝑖𝑜𝑛 𝑎𝑛𝑑 𝑡𝑟𝑎𝑛𝑠𝑚𝑖𝑠𝑠𝑖𝑜𝑛 𝑜𝑓 𝑡ℎ𝑒 ℎ𝑢𝑚𝑎𝑛 𝑚𝑖𝑐𝑟𝑜𝑏𝑖𝑜𝑚𝑒”

Segata Lab
@cibiocm.bsky.social

#proudteam here! Nicola Segata received the Charles Donovan Microbiome Prize.

APC Microbiome Ireland@apcmicrobiomeirel.bsky.social

Moderator and APC Director Prof Paul Ross presented the Charles Donovan Microbiome Award to Nicola. @cibiocm.bsky.social #APCSymposium2026 #APCMicrobiomeIreland #Microbiome #CharlesDonovan

Segata Lab
@cibiocm.bsky.social

🎉 Exciting news from our lab! cFMDv1.3.2 is now live. This release marks a significant expansion of cFMD: 📊 681 newly integrated food metagenomes from 22 public datasets 18,180 total MAGs across 4,125 metagenomes 54 countries (now including 🇲🇦) 100+ food-related studies 1/3

Segata Lab
@cibiocm.bsky.social

🌍 New additions: • Novel food types: Korean rice vinegar, yucha, and more • Expanded profiling of fruits, vegetables, and meats • Enhanced geographic representation 2/3

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Segata Lab
@cibiocm.bsky.social

📌 The most transmissible gut species are associated with poorer cardiometabolic health and enriched for T2 diabetes biomarkers, possibly because the traits that allow them to thrive in inflammatory disease are the same ones that help them survive the journey between humans 4/n

Segata Lab
@cibiocm.bsky.social

📌 In 75% of cases where the same species was detected in both oral and gut environments of the same individual, it was the same strain, pointing to saliva-mediated oral-to-gut transmission as a dominant mechanism Find more in the paper: www.cell.com/cell-press-b... 5/n

cell.comStrain transmission links human microbiomes along the oral-gut axis and across cohabiting individualsHeidrich and colleagues analyzed paired oral and fecal metagenomes to map the inter-connectedness of human microbiomes across body sites and cohabitants. The work reveals high inter-personal transmiss...
Segata Lab
@cibiocm.bsky.social

We analyzed paired oral and fecal metagenomes from hundreds of cohabiting individuals to map microbial strains traveling between people and body sites. Read key findings below: 2/n

Segata Lab
@cibiocm.bsky.social

📌 Cohabitants share significantly more oral and gut strains than non-cohabiting individuals across all relationship types 📌 Likely driven by kissing, romantic partners show the highest oral microbiome sharing 📌 Oral strains are more frequently replaced than gut strains 3/n

Segata Lab reposted

Binning Singletons
@binningsingletons.com

We have an unusual situation this year: we have more mentors than usual for our current number of Singletons! Please share the link with your network! We will match up as many as we can! #ASMicrobe #MicroSky 🦠🧪🔬

Binning Singletons@binningsingletons.com

Microbe @asm.org attendees! The matching registration form is locked but you can still join the community! forms.gle/5roddkPnjuBt... Join us on Slack and IRL. We often gain up to an additional 50% more people after we've made matches! #ASMicrobe #MicroSky 🔬🧪🦠🏳️‍🌈

forms.gleBinning Singletons RegistrationPlease complete ONLY if you are attending #ASMicrobe in Washington, DC, June 4-7, 2026 Singletons Looking for community and inclusion at ASM Microbe this year? Join other Singletons (first-time and s...
Segata Lab
@cibiocm.bsky.social

#IHMC2026 starts this week in Seoul 🇰🇷 If you're attending, do not miss to hear more about our work from: @vheidrich.bsky.social who will be presenting the poster [ABST-000189, P1-024]: Improving Bacterial Strains Reconstruction and Microbiome Transmission Inference from Metagenomes 1/2

Segata Lab reposted

Svetlana Ugarcina Perovic
@svetlanaup.bsky.social

New #MicrobiomeDigest is OUT microbiomedigest.com/2026/05/29/m... • root microbiome/ @algazuccaro.bsky.social   • gut microbiome-epigenetics/ @gangfang.bsky.social   • resistome annotation/ @bigdatabiology.bsky.social   • invitation for #MVIF 50🎂 / @microbiomevif.bsky.social & more. Happy Friday!

microbiomedigest.comMay 29, 2026See you next week at MVIF! Global microbiome Advancing microbial ecology, microbiomes, and One Health in Africa: From regional initiatives to pan-African flagship programs – Mohamed Hijri – The ISM…

Segata Lab reposted

Segata Lab
@cibiocm.bsky.social

#MeetTheLab @msabrysarhan.bsky.social works on his postdoc (joint w/ #EURAC) on ancient diet & microbiomes. How to overcome failure in science? I like a lot what Robert Frost said: "Two roads diverged in a wood, and I— I took the one less traveled by, And that has made all the difference."

Segata Lab reposted

bigdatabiology.bsky.social
@bigdatabiology.bsky.social

How well do ARG detection pipelines agree when applied to the same data? Spoiler: not very well. In our new preprint, we ran 10 pipelines on 270M microbial unigenes from GMGCv1. The same data can support conflicting biological conclusions! 🧵 www.biorxiv.org/content/10.6...

biorxiv.orgThe elusive resistome: a global comparison reveals large discrepancies among detection pipelinesIdentifying antibiotic resistance genes (ARGs) from metagenomic data is critical for studying antimicrobial resistance across microbial communities and pathogens. However, there is no standardized methodology for ARG annotation. Here, we compare ten commonly used ARG detection pipelines by analysing over 270 million prokaryotic genes from the Global Microbial Gene Catalogue across 13 distinct habitats. We observed up to a 45-fold difference in the number of reported ARGs, with a mean Jaccard index of only 16% between pipelines. Pipeline selection profoundly impacted downstream biological interpretations, with drastic changes to estimates of ARG relative abundance and richness, to the characterization of pan- and core-resistomes, and to the class-level composition of the inferred resistome. ARG detection pipelines make different, defensible trade-offs, and no single approach should be treated as authoritative. Therefore, users should justify and communicate choices carefully, as our analyses show that, taken uncritically, the same data can support conflicting biological and ecological interpretations. ### Competing Interest Statement The authors have declared no competing interest. National Health and Medical Research Council of Australia (NHMRC), 2031902 Australian Research Council (ARC), FT230100724 International Development Research Centre (IDRC), 109304-001 Deutsche Forschungsgemeinschaft (DFG), FO1279/6-1 Bundesministerium für Bildung und Forschung (BMBF), F01KI1909A, 01KI2404B Swedish Research Council (VR), 2024-06123, 2019-00299, 2023-01721 Knut and Alice Wallenberg Foundation, KAW 2020.0239 Swedish Foundation for Strategic Research, FFL21-0174

Segata Lab reposted

Youssef El Mouali
@youssefelmouali.bsky.social

New paper out in @cp-cellhostmicrobe.bsky.social! Microbes evolving with modern lifestyles 🧬🦠 S. copri uses PerR to manage oxygen stress, but some strains acquired OxyR via HGT, boosting oxygen tolerance. These strains are enriched in industrialized populations. www.cell.com/cell-host-mi...

cell.comBiogeography-associated emergence of enhanced oxygen tolerance in the abundant human gut commensal Segatella copriEl Mouali and Tawk et al. characterize the oxygen-tolerance response in the human gut-residing bacterium Segatella copri. They identified a subset of strains that acquired an additional oxygen regulat...

Segata Lab reposted

Svetlana Ugarcina Perovic
@svetlanaup.bsky.social

NEXT WEEK Chioma Onyido and I are happy to be part of #IBC2026 where we will share our #BugSigDB @bioconductor.bsky.social experience!

International Biocuration Conference 2026@intbioconf2026.bsky.social

🧬 Workshop @ #IBC2026 | Cape Town Community-Driven Biocuration for Microbiome Research 📅 Apr 20, 2026 | 👩‍🔬 Dr S. Ugarcina Perovic & Ms Chioma Oselu ⚠️ Conference registration required 📝 Register: www.bioinformaticsinstitute.africa/form/worksho...