Microbiome Research @SunagawaLab
Microbiome Research Lab at the Institute of @Microbio_ETH Zurich | Tweets by lab members micro.biol.ethz.ch/research/sunag… Zürich, Switzerland Joined March 2019-
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This work is here thanks to @emily_fogarty11, whose dedication turned a surprising observation into a piece of science. But many others helped us push it forward. @sandralmclellan, @KarenLolans, @mschecht_bio, @AmyDWillis, @SunagawaLab, Laurie Comstock et al, THANK YOU ALL :)
A reminder for ECRs who are looking for an opportunity to form their own group to study contemporary questions in marine sciences in Germany with 5-years of support: hifmb.de/focus-group-ca…
New computational tools from @SunagawaLab @NCCRMicrobiomes 👏 mBARq: a versatile and user-friendly framework for the analysis of DNA barcodes from transposon insertion libraries, knockout mutants and isogenic strain populations biorxiv.org/content/10.110…
I'm excited to share that I've accepted a position as Professor for #environmental #microbiology at @uniinnsbruck in Austria. My lab will focus on microbial omics of uncharacterised taxa and on plastic biorecycling. Will post job ads shortly - for 2x PhD and 1x postdoc
Predicting interactions in plant microbiomes made possible. Metabolic modelling sheds light on bacterial interactions in planta, see the recent work by Vorholt Lab @ETH_en and @realLCSB at EPFL. More: doi.org/10.1126/scienc…
What is #EMBLtrec about? Why did we embark on a journey along the European coastlines? What are the scientific questions we are studying? Watch our new video to find out! youtube.com/watch?v=yky1kz… @embl @TaraOcean_ @EMBRC_EU 📸 Kinga Lubowiecka / EMBL
We're hiring for a postdoc position focused on metabolic modeling. Please share widely.
The huge success of #HIFMBsymposium's session 3 on the multi-data matrix behind functional biodiversity are attributed to: Linda Amaral Zettler @plasticphere, Shinichi @SunagawaLab, Kirsten Küsel @idiv and Boris Koch @AWI_Media #thankyou #microorganisms #chemodiversity
So many creative ideas and forward looking plans at the 2nd symposium on federating bioinformatics tools and resources last week. Truly thrilled to be part of this group of scientists
🐠 Un trésor à explorer, chérir et protéger l.geo.fr/mz4
@GenomeBiology @TaraOcean_ @nanopore Here a research highlight of the Tara Pacific program involved a two-year continuous scientific expedition at sea to reveal new facets of coral reef biodiversity in the Pacific Ocean go.nature.com/42j0Dbb
Breaking! #TaraPacific expedition: We integrate genomic, transcriptomic, and environmental data to describe symbiotic fidelity and plasticity in Pocillopora across the Pacific. An all star team and incredible #OpenAccess dataset! nature.com/articles/s4146… @GenoLAGE @TaraOceans_Sci
Today get out the results of a 7 years marathon around the Tara Pacific expedition. In a collection of 8 papers (nature.com/collections/ad…) and more to come.
The Tara Pacific program involved a two-year continuous scientific expedition at sea to reveal new facets of coral reef biodiversity in the Pacific Ocean. This Collection highlights research published from this ambitious project. go.nature.com/42j0Dbb
new work TaraPacific expedition: #OpenAccess environmental, chemical, physical, etc metadata for 249 coral reef locations detailing ~58,000 samples => dream dataset to go correlation hunting & identify predictors nature.com/articles/s4159… @UniKonstanz kudos to all & @TaraOceans_Sci
1/9 new works: 7 years ago we embarked to describe biodiversity of Pacific coral reefs w/ @TaraOceans_Sci using standardized sampling: 100,000km sailing, 3,000 dives, 50,000samples. Today we are happy to announce first outcomes, summary: nature.com/articles/s4146… @UniKonstanz
the Tara Ocean Foundation @TaraOcean_ @TaraOceans_Sci has launched a poll to gather opinions on their first 20 year's of activities technopolisfr.limesurvey.net/174239?lang=en. Please participate, share, and help shape their next 20 years !
Find out how new @HorizonEU funding for @BlueRemediomics will help researchers better understand marine microbiomes and uncover new bioresources to strengthen the blue economy. #BlueRemediomics ebi.ac.uk/about/news/ann…
Cameron Thrash @jcamthrash
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Marnix Medema @marnixmedema
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Michael Zimmermann La.. @Zimmermann_Lab
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Carlos Iglesias-Aguir.. @cigaguirre
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Tolga Tarkan Olmez, P.. @tolgatarkanlme2
33 Followers 857 Following BSc @BilkentMBGDept Phd @bilkentunam postdoc @MCDB_Yale Expert: synbio, sys. bio., bioeng, biomed. Incoming asst. prof. @baskentunv Lang: TUR/ENG
FRED @FREDEDUARDOHER1
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Miriam Kronen @MIriam__KRO
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Alex (Chen Zhang) @Tsins361158385
313 Followers 1K Following A microbiology researcher, and believe they are in power dimensionally. A traveler from Asia (🇨🇳) to Europe (🇳🇱), and now in America (🇺🇸). Move Forward!
Camilo García @Gaspardelanoche
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David VG @pDavidVG97
126 Followers 371 Following Avid Jeopardy! fan. Grad student at UIUC. Interested in symbiosis and co evolution @ the Heath lab. UCSD alumn. He/him
Anh Van Le @AnhVan_Le
360 Followers 842 Following Postdoc in Environmental microbiology at ISWA @Uni_Stuttgart
Arzum @arzumnurgursoy
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Qiyun Zhu @zhuqiyun
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Mitiku Mihiret Seyoum @Seyoum90
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Oleksandr Narykov �.. @onarykov
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Cameron Thrash @jcamthrash
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Marnix Medema @marnixmedema
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Elisa Granato @Prokaryota
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Akos T. Kovacs @EvolvedBiofilm
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Michael Zimmermann La.. @Zimmermann_Lab
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Maier_Lab @lab_maier
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Jonathan Eisen @phylogenomics
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ETH Zurich @ETH_en
92K Followers 552 Following This is the official Twitter account of ETH Zurich in English. Stay tuned for the latest news on research, technology and education. Deutscher Account: @eth
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Flora Vincent @vincentflora
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208 Followers 204 Following PhD Student @Piel_Lab @ETH Visiting Student @Drennan_Lab @MIT Olympian from Liechtentstein
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112 Followers 111 Following
EMBLtrec @EMBLtrec
1K Followers 82 Following Traversing European Coastlines will study coastal ecosystems & their response to the environment: sea and land research, public engagement and outreach.
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Leão Lab - CIIMAR (U.. @leao_lab
817 Followers 562 Following Cyanobacterial natural products chemistry, biosynthesis & ecology Run by lab members!
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Melanie Stäubli @melaniestaeubli
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Jan Brüwer @JanBruewer
363 Followers 303 Following Phd student @marinemicrobio & @MolEcolMPIMM using the 🔬 to Study bacterial growth and their viruses. discoverer of zombies 🧟♂️ // scuba diver 🤿, sailor ⛵️
Helene Morlon @HMorlon
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The ISME Journal @ISMEJournal
12K Followers 381 Following Journal of the International Society for Microbial Ecology
GTDB @ace_gtdb
2K Followers 0 Following The Genome Taxonomy Database (GTDB) is a standardised microbial taxonomy based on genome phylogeny.
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Harihara Subrahmaniam.. @Harihara_subrah
140 Followers 1K Following Grad Student @umdcs. Research in Bioinformatics and Computational Biology. Algorithms for Microbiomics with Prof. Mihai Pop.
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Doudna Lab @doudna_lab
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Nikos Kyrpides @kyrpides
2K Followers 568 Following Microbiome, Virome, Bioinformatics, Big Data, Data Science, Open Data, Open Science, “Opinions are mine" #bringthembackcrash course on "the coral microbiome in sickness, in health, and in a changing world", specifically addresses how climate change affects biology & guides future research! kudos to all coauthors! @UniKonstanz @NatureMicrobiol rdcu.be/dAiZe
This work is here thanks to @emily_fogarty11, whose dedication turned a surprising observation into a piece of science. But many others helped us push it forward. @sandralmclellan, @KarenLolans, @mschecht_bio, @AmyDWillis, @SunagawaLab, Laurie Comstock et al, THANK YOU ALL :)
I am happy to report that @michaelkuyu and @emily_fogarty11's work that adds more structure to our desire to understand naturally occurring plasmids is now online at @NatureMicrobiol 🎉 nature.com/articles/s4156…
@alvarordr, lead author of the paper, made a nice thread with a more detailed summary of our findings. Check it out if interested!👇
Extremely excited to share that our effort to identify and characterize Functionally and Evolutionarily Significant Novel (FESNov) gene families exclusive of uncultivated taxa is now published in @Nature nature.com/articles/s4158… @jhcepas @cgmlaboratory 🧵with main findings 👇
But this final version comes with quite some updates! We have extended our functional predictions & included a new section on biomarker discovery.
Guided by the genomic architecture of known function genes, we could calibrate our genomic context functional predictions, and assign >4k FESNov gene families to key microbial pathways with high confidence.
In collaboration with Emilia López Solanilla’s lab, we validated some of our functional predictions in vitro. First, we demonstrated that a FESNov gene family located in the che operon is involved in cell motility.
We also show that a small peptide, located close to several antibiotic resistance genes & showing antimicrobial motifs, inhibits the growth of several Gram positive bacteria.
We also predicted protein structures of almost all the 400k families, which allowed us to gather functional predictions for ~56k FESNov gene families, complementing our genomic context predictions. These structures are available at modelarchive.org/doi/10.5452/ma…
We have also conducted an analysis on the impact of incorporating these families into microbiome analysis. We demonstrate that FESNov gene families contribute to a better discrimination of clinical conditions (e.g. CRC) and include markers of the disease.
Overall, given their relevance, we conclude that FESnov gene families should be considered in microbiome studies. For such purpose, we have incorporated them into eggnog mapper eggnog-mapper.embl.de, which now allows to profile FESNov gene families in any genome or metagenome
We have also improved our online server for the exploration of the genomic context of the FESNov gene families (novelfams.cgmlab.org), which now include new features such as fast sequence searches
This would have been impossible without the contributions of many people, both from the @CBGP_Madrid @cgmlaboratory (@jhcepas @Ginerorama @cpcantalapiedra @deng_ziqi @anahernandezpl1 @jbotas2) & Lopez-Solanilla’s lab
Extremely excited to share that our effort to identify and characterize Functionally and Evolutionarily Significant Novel (FESNov) gene families exclusive of uncultivated taxa is now published in @Nature nature.com/articles/s4158… @jhcepas @cgmlaboratory 🧵with main findings 👇
Our study on the biological relevance of novel microbial gene families is out today. Peer review & comments really improved our 2022 preprint: better func. predictions, experimental validations, structural models & impact on microbiome association studies. nature.com/articles/s4158…
and from different groups around the globe @SunagawaLab @BorkLab @luispedrocoelho Thanks a lot and congratulations!
This was an awesome work by @alvarordr, @Ginerorama and many other members of the @cgmlaboratory, in collaboration with friends and colleagues from the Lopez-Solanilla lab at @CBGP_Madrid, @BigDataBiology lab, @BorkLab and @SunagawaLab. Thank you all for the great work!
Researchers @Lcs_Paoli and @SunagawaLab at @Microbio_ETH used metagenomic analysis to uncover biosynthetic potentials in previously uncharacterized microorganisms, revealing an active underwater “pharma-sea.” @KristelTjandra reports. ow.ly/g4WM50PWGPJ
Many ppl contribute(d) to SPIRE, including @luispedrocoelho & team, @pam_ferretti @olex_maistrenko @AskarbekOrakov @pangenomics @SunagawaLab @robdfinn and of course members of @BorkLab, among several others.
I'm excited to share that I've accepted a position as Professor for #environmental #microbiology at @uniinnsbruck in Austria. My lab will focus on microbial omics of uncharacterised taxa and on plastic biorecycling. Will post job ads shortly - for 2x PhD and 1x postdoc
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