Samir Giri
Postdoctoral Fellow @TypasLab @EMBLHeidelberg
Interested in ecology and evolution of microbial communities, microbiome, culturomics, experimental (co)evolution, microbiome modulation
🦠🧫🔬🧪💊💩🧬
scholar.google.com/citations?user=dhZf…
- Reposted by Samir GiriExcited to announce my upcoming @snsf.ch Ambizione research group at EPFL on bacteria-host interactions, combining systems approaches and microphysiological models. 🚨 We have an open PhD position! More info on projects and how to apply here: elisabettacacace.github.io/BHI-Lab/ 🧪
- Reposted by Samir GiriProtists shift bacterial interactions Soil protist predation shifts bacterial metabolic interactions from competitive to cooperative. Protist-driven microbial cross-feeding enhances plant-beneficial functions www.cell.com/cell-host-mi...
- Reposted by Samir GiriIt has been two weeks since the unexpected death of Peer Bork, and all of us in his research group are deeply missing him. His scientific vision brought us together as a team, and we are immensely grateful for the time we spent together. 🧵
- EMBL is deeply saddened by the passing of our Interim Director General Peer Bork, a pioneering scientist who left an indelible imprint on life science research in Europe and beyond. We extend our deepest condolences to his family, friends, and colleagues. www.embl.org/news/people-...
- Reposted by Samir GiriNow online! A Bacteroides synthetic biology toolkit to build an in vivo malabsorption biosensor
- Reposted by Samir GiriPeer Bork died yesterday 💔 which shocked me. In 2003 I did a short-term fellowship in Peer’s lab because I idolized him. I met Martin there & we wrote this paper together. Peer was great at bringing people together; a master collaborator with a rare ability to think up big ideas.
- Reposted by Samir GiriThis is such hard news to process. Such an amazing scientist and inspiration for so many of us. www.embl.org/news/embl-an...
- Reposted by Samir GiriNature research paper: Genetic switch between unicellularity and multicellularity in marine yeasts go.nature.com/4poZ9HP
- Reposted by Samir Giri"The changing roles of Escherichia coli" -- a short essay by yours truly. rdcu.be/eVtXT
- Reposted by Samir GiriThis broader metabolic capacity makes core microbes true functional generalist with far greater metabolic independence than non-core taxa, allowing them to thrive in the dynamic rumen environment. (4/8)
- Reposted by Samir GiriExcited to share our new @natecoevo.nature.com paper. We identified microbes found across nearly all ruminants that act as the functional backbone of both the rumen ecosystem and the host, with major implications for food security and climate change mitigation. (1/8) www.nature.com/articles/s41...
- Reposted by Samir GiriLong read Metagenomics, #phage and #prophage in the gut by Ami Bhatt's group. Beautiful data showing changes in phages over two years #phagesky www.nature.com/articles/s41...
- Reposted by Samir GiriCombining genome-scale metabolic modelling with in vitro and in planta experiments, the authors show that cross-feeding metabolites and substrate utilization synergistically determine microbial community resistance to pathogen invasion 🧪 www.nature.com/articles/s41...
- Reposted by Samir GiriHighlighting another recent paper from the lab in Science Advances on engineering a gut probiotic to modulate GLP-1 levels and ameliorating colitis. Led by Leonie Brockmann & @carlottaronda.bsky.social . @columbiasysbio.bsky.social @columbiauniversity.bsky.social 🧬🦠💊 www.science.org/doi/full/10....
- Reposted by Samir GiriPopulation genetics simulations and analysis of experimental datasets in yeast, Drosophila and E. coli show that beneficial mutations are abundant but transient, as they become deleterious after environmental turnover (antagonistic pleiotropy)🧪 www.nature.com/articles/s41...
- Reposted by Samir GiriHmmm This work has so many implications on literature 😳😬 Fluorescein-based dyes are not valid reporters of oxidative stress in bacteria, and conclusions based on their use must be reconsidered | PNAS www.pnas.org/doi/10.1073/...
- Reposted by Samir GiriFecal exfoliome sequencing captures immune dynamics of the healthy and inflamed gut - @harriswang.bsky.social go.nature.com/4i7XnZR
- Reposted by Samir GiriNiche partitioning by resource size in the gut microbiome biorxiv.org/content/10.1101/202…
- Reposted by Samir GiriWhen colonizing a new habitat, organisms adapt to maximize their reproductive success via #LifeHistory #evolution. @ecoevodevolab.bsky.social @cbank.bsky.social show that life history evolution facilitates niche diversification across a range of theoretical models @plosbiology.org 🧪 plos.io/4p7YT0a
- Reposted by Samir GiriVery excited to share our latest work in Science on metagenomic editing (MetaEdit) of the gut microbiome in vivo & directly modifying unculturable immune-modulatory SFB bug in the small intestine. 🦠🧬🛠️ www.science.org/doi/10.1126/...
- Reposted by Samir GiriMetagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases | Science
- Reposted by Samir Giri@sacrozhangt.bsky.social and I wrote a commentary on Jordi van Gestel and Carol Gross's latest paper, check it out! www.pnas.org/doi/10.1073/... Sadly, the Editors at PNAS rejected our initial introduction, which was a David Attenborough style voice over of the microbial Serengeti (included below)
- Reposted by Samir GiriLet me use this as an opportunity to talk about Jordi et al's very cool paper, now out in PNAS 🧪: pmc.ncbi.nlm.nih.gov/articles/PMC... You can read our news and views here: www.pnas.org/doi/10.1073/...
- @sacrozhangt.bsky.social and I wrote a commentary on Jordi van Gestel and Carol Gross's latest paper, check it out! www.pnas.org/doi/10.1073/... Sadly, the Editors at PNAS rejected our initial introduction, which was a David Attenborough style voice over of the microbial Serengeti (included below)
- Reposted by Samir GiriSuper excited that the bulk of my PhD work is now preprinted! Here we used whole-community competition, or coalescence, experiments to quantify selection acting on genetically diverged strains within larger communities. (1/n) www.biorxiv.org/content/10.1...
- Reposted by Samir GiriCan we leverage bacterial competition for targeted replacement of harmful strains? Maybe! Our recent piece in @natmicrobiol.nature.com provides a theoretical framework and a set of experiments to show what it might take: www.nature.com/articles/s41...
- Reposted by Samir GiriHad to draw a cartoon for this fascinating finding! Defensive fungal symbiosis on insect hindlegs: www.science.org/doi/10.1126/... #SymbioSky
- Reposted by Samir Giri@prczhaoyansong.bsky.social’s deep dive into the dark matter of compost communities is now out 🎉 Genomic islands hijack jumbo phages—whose capsids enable transfer of large tracts of DNA—shedding new light on the scale & scope of phage-mediated gene flow 😎 www.pnas.org/doi/10.1073/...
- What makes PhD students happy? Good supervision Supportive and frequent supervision is a key factor that significantly enhances PhD students' satisfaction and well-being during their research journey. doi.org/10.1038/d415...
- Reposted by Samir GiriNEW publication from our lab: One of the first methodologies (FUGAsseM) for gene function prediction from microbial community multi-omics data! www.nature.com/articles/s41... 🧵⬇️ 1/8
- Reposted by Samir GiriOUT NOW Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism by @ryanziels.bsky.social www.nature.com/articles/s41...
- Reposted by Samir GiriExcited to share our LongTrack study out in @natmicrobiol.nature.com today! Fecal microbiota transplant (FMT), donor 💩 => patients' gut, is an effective treatment for recurrent C. difficile infection & is being evaluated for Inflammatory Bowel Diseases (IBD) & other conditions 1/ 📄 rdcu.be/eL8mR
- Reposted by Samir GiriOur @narjournal.bsky.social manuscript is out! It explores the growth of the GTDB (gtdb.ecogenomic.org) since its inception, as well as updates to the website, methodology, policies, and major taxonomic and nomenclatural changes over the past three years. academic.oup.com/nar/advance-...
- Cool new method, LongTrack for long-read metagenomics, to accurately track high-resolution microbial strains after faecal microbiota transplant, revealing detailed, long-term engraftment patterns rdcu.be/eMcNg
- Reposted by Samir GiriNew paper with my (amazing) friend and mentor @jrpenades.bsky.social Really looking forward to see what plasmid aficionados think of this one!! With @asantoslopez.bsky.social @wfigueroac3.bsky.social Akshay Sabins and others www.cell.com/cell-reports...
- Reposted by Samir GiriPlease share this with anyone who may be interested in a post-doc in Germany: jobs.awi.de/Vacancies/20... This is quite an exciting opportunity to push the boundaries of what is known regarding the molecular basis of the formation and demise of photosymbiotic relationships in marine habitats.
- Reposted by Samir GiriVery excited to share the latest work from our lab, which was published today in Nature! nature.com/articles/s41... PhD graduate and now post-doc Sofia Dahlman, along with co-senior author Sam Forster from The Hudson and other researchers from our lab and others.
- Reposted by Samir GiriHere's the link to the system, try it! qedscience.com @qedscience.bsky.social
- Reposted by Samir GiriPredicting functions of uncharacterized gene products from microbial communities www.nature.com/articles/s41... #jcampubs
- Reposted by Samir GiriExcited to share our preprint led by Carlos Voogdt et al We developed new genetic tools & genome-wide libraries for species of the Bacteroidales order; constructed saturated barcoded transposon libraries in key representatives of three genera. www.biorxiv.org/content/10.1...
- New Preprint from Voogdt et al 👇 Establishes efficient genome-wide transposon mutagenesis & barcode mutant libraries for three Bacteroidales gut bacteria, identifying shared & species-specific essential genes, non-coding elements, & toxin pathways, advancing gut microbiome functional genomics
- A toolkit for transposon libraries and functional genomics in intestinal Bacteroidales biorxiv.org/content/10.1101/202…
- Reposted by Samir Giri
- Reposted by Samir GiriNow online! A chemical radar allows bacteria to detect and kill predators
- Reposted by Samir Giri#Perspective Estrela and Huang discuss nutrient starvation in the context of the gut microbiome, outlining what is known and highlighting key questions for future research to address knowledge gaps. #MicroSky #MicrobiomeSky 🦠 www.nature.com/articles/s41...
- Reposted by Samir GiriThe Vienna BioCenter PhD Program application deadline is approaching: October 10! Join one of Europe’s premier life science campuses, home to cutting-edge research across all areas of biology. Apply and start your scientific journey in Vienna! training.vbc.ac.at/phd-program/ #PhD #LifeSciences
- Love RNA biology? Join us to explore the piRNA pathway with structural and genetic approaches (see 👇👇). PhD student/postdoc position co-supervised by Clemens Plaschka & myself. DM or email us if you’d like to know more! @vbcscitraining.bsky.social @imbavienna.bsky.social @impvienna.bsky.social
- Reposted by Samir GiriNew pre-print: Eco-evolutionary responses of phage to different thermal regimes. Great work led by Sam Greenrod and fun collaboration with Kayla King's lab. 1/2 www.biorxiv.org/content/10.1...
- Reposted by Samir GiriA ghost in the machine? It appears when parts merge, a new logic takes hold, and a higher-level individual emerges. Life showed it in eukaryogenesis. Humans and AI could unwittingly stumble into something similar.
- Opinion: As human–AI interdependence deepens, could they form an integrated evolutionary individual, subject to collective selection? Explore this perspective in PNAS Front Matter: www.pnas.org/doi/10.1073/... #AI #evolution #singularity #ChatGPT #LLM #MajorEvolutionaryTransition
- Reposted by Samir GiriCool PNAS paper by @jordivangestel.bsky.social and colleagues Contributed by Carol Gross [reviewed by @polzlab.bsky.social and @wcratcliff.bsky.social] Bacillus subtilis in defense mode: Switch-like adaptations to protistan predation www.pnas.org/doi/10.1073/...
- Reposted by Samir GiriDelighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols. Thread 1/n
- Reposted by Samir GiriExcited to share our @cp-cellhostmicrobe.bsky.social led by Magda showing how Bif has co-evolved with different animal hosts 🐒🐭🐷🐦 Key takeaways: 🔹 Host ancestry + diet shape Bif evolution 🔹 Mammals enriched for carb-busting enzymes 🔹 Untapped diversity in non-human hosts = new probiotic potential
- Bifido adaptations across hosts @halllab.bsky.social survey insects, reptiles, birds & mammals to uncover how Bifidobacterium adapts to hosts. Bifidobacterium & host exhibit strong co-phylogenetic associations, driven by vertical transmission & dietary selection www.cell.com/cell-host-mi...
- Unusual reproductive strategy in Iberian harvester ants challenges the conventional biological boundaries that define "species" as one queen effectively produces two genetically distinct species (into males of their own species and males of another species) within a single colony 😲👇
- Nature research paper: One mother for two species via obligate cross-species cloning in ants go.nature.com/45PYV6d
- Reposted by Samir GiriNature research paper: Commensal yeast promotes Salmonella Typhimurium virulence go.nature.com/4mTnRzG
- Reposted by Samir GiriNice interview to Katie Peichel @currentbiology.bsky.social I completely agree with her claims for more funding for curiosity-driven research, basic Science... Science. www.cell.com/current-biol...
- Reposted by Samir GiriMicrobiomes are interactive, multispecies communities, but bulk analysis obscures functional diversification from environmental and genetic heterogeneity. In our new review we describe how single-bacterium transcriptomics dissects microbiomes at cellular resolution. www.science.org/doi/10.1126/...
- Reposted by Samir GiriNature research paper: One mother for two species via obligate cross-species cloning in ants go.nature.com/45PYV6d
- Reposted by Samir GiriEngineering Synthetic Phase Variation for Control of Microbial consortium biorxiv.org/content/10.1101/202…
