Samir Giri
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isamirgiri.bsky.social
Samir Giri
@isamirgiri.bsky.social
590 followers 720 following 46 posts
Postdoctoral Fellow @TypasLab @EMBLHeidelberg
Interested in ecology and evolution of microbial communities, microbiome, culturomics, experimental (co)evolution, microbiome modulation
🦠🧫🔬🧪💊💩🧬

https://scholar.google.com/citations?user=dhZfxqMAA
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isamirgiri.bsky.social
Samir Giri @isamirgiri.bsky.social · Jan 13
Excited to share our opinion piece with the KC Huang Lab.
Check it out here:
Harnessing gut microbial communities to unravel microbiome functions
doi.org/10.1016/j.mi...
@typaslab.bsky.social
Reposted by Samir Giri
erikbakkeren.bsky.social
Can 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...
Strain displacement in microbiomes via ecological competition - Nature Microbiology
Mathematical modelling and experimental tests reveal principles that govern displacement of a resident strain by an invader in microbial communities.
www.nature.com
November 7, 2025 at 10:34 PM
Reposted by Samir Giri
chaintist.bsky.social
Had to draw a cartoon for this fascinating finding!
Defensive fungal symbiosis on insect hindlegs: www.science.org/doi/10.1126/...
#SymbioSky
A cartoon/ digital drawing summarising the findings of the paper "Defensive fungal symbiosis on insect hindlegs" by T. Nishino et al published in 2025. On the top left, a female Megymenum gracilicorne bug shows off symbiotic organs on the hind legs where she carries Ascomycota fungi. These were previously assumed to be Tympanal organs in these bugs but only females had them?; that didnt make a whole lot of sense to the authors...To the right of the bug is a row of eggs lying side by side. The paper shows that the bugs deposit the symbiotic fungi on the egg surface after egg-laying. Next on the image, fungal conidia grow on the egg surface. The eggs are pinkish in colour. A few fungi wear sunglasses like they are body guards. The paper shows that they protect the eggs from Trissolcus brevinotaulus, a parasitoid wasp, that likes to lay its eggs inside the developing bug's eggs. There are two wasps in this cartoon "eyeing" the fungi and looking frustrated. Eggs turn from whitish to pinkish within 10-days because they are reflecting the body colour of the nymph within the eggs.
November 1, 2025 at 4:59 PM
Reposted by Samir Giri
paulbrainey.bsky.social
@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/...
Jumbo phage–mediated transduction of genomic islands | PNAS
Bacteria acquire new genes by horizontal gene transfer, typically mediated by mobile genetic elements (MGEs). While plasmids, bacteriophages, and c...
www.pnas.org
October 28, 2025 at 6:36 PM
isamirgiri.bsky.social
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...
October 24, 2025 at 4:55 PM
Reposted by Samir Giri
hutlab.bsky.social
NEW 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
Predicting functions of uncharacterized gene products from microbial communities - Nature Biotechnology
FUGAsseM predicts protein function in microbiomes using coexpression patterns from metatranscriptomes and diverse community-wide data.
www.nature.com
October 23, 2025 at 6:53 PM
Reposted by Samir Giri
natmicrobiol.nature.com
OUT NOW Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism by @ryanziels.bsky.social www.nature.com/articles/s41...
Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism - Nature Microbiology
An approach combining BONCAT, stable isotope probing and metaproteomics showcases the hidden metabolic interconnectivity of microorganisms within an anaerobic digestion community.
www.nature.com
October 21, 2025 at 1:38 PM
Reposted by Samir Giri
gangfang.bsky.social
Excited 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
Long-read metagenomics for strain tracking after faecal microbiota transplant
Nature Microbiology - A long-read metagenomics method empowers faecal microbiota transplantation studies by precisely tracking bacteria from donors to recipients, distinguishing co-existing strains...
rdcu.be
October 22, 2025 at 3:39 PM
Reposted by Samir Giri
ace-gtdb.bsky.social
Our @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-...
GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes
Abstract. The Genome Taxonomy Database (GTDB; https://gtdb.ecogenomic.org) provides a phylogenetically consistent and rank normalized genome-based taxonomy
academic.oup.com
October 22, 2025 at 2:20 PM
isamirgiri.bsky.social
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
Long-read metagenomics for strain tracking after faecal microbiota transplant
Nature Microbiology - A long-read metagenomics method empowers faecal microbiota transplantation studies by precisely tracking bacteria from donors to recipients, distinguishing co-existing strains...
rdcu.be
October 22, 2025 at 3:10 PM
Reposted by Samir Giri
sanmillan.bsky.social
New 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...
Non-conjugative plasmids limit their mobility to persist in nature
Sabnis et al. explain why non-conjugative plasmids move at a low rate in nature. While increased mobility can easily evolve by incorporating phage DNA into plasmids, this is disadvantageous because it...
www.cell.com
October 22, 2025 at 1:12 PM
Reposted by Samir Giri
merenbey.bsky.social
Please 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.
October 22, 2025 at 10:36 AM
Reposted by Samir Giri
jeremyjbarr.bsky.social
Very 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.
Isolation, engineering and ecology of temperate phages from the human gut - Nature
Human host-associated cellular products may act as induction agents for bacteriophages.
nature.com
October 15, 2025 at 9:41 PM
Reposted by Samir Giri
odedrechavi.bsky.social
Here's the link to the system, try it! qedscience.com
@qedscience.bsky.social
q.e.d Science
Critical Thinking AI for constructive criticism and science evaluation
qedscience.com
October 15, 2025 at 12:22 PM
Reposted by Samir Giri
jcamthrash.bsky.social
Predicting functions of uncharacterized gene products from microbial communities www.nature.com/articles/s41... #jcampubs
Predicting functions of uncharacterized gene products from microbial communities - Nature Biotechnology
FUGAsseM predicts protein function in microbiomes using coexpression patterns from metatranscriptomes and diverse community-wide data.
www.nature.com
October 15, 2025 at 3:17 PM
Reposted by Samir Giri
typaslab.bsky.social
Excited 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...
October 13, 2025 at 7:48 AM
isamirgiri.bsky.social
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
October 11, 2025 at 5:43 PM
Reposted by Samir Giri
cbo.bsky.social
www.pnas.org/doi/10.1073/...
In vivo directed evolution of an ultrafast Rubisco from a semianaerobic environment imparts oxygen resistance | PNAS
Carbon dioxide (CO2) assimilation by the enzyme Ribulose-1,5-bisphosphate Carboxylase/Oxygenase (Rubisco) underpins biomass accumulation in photosy...
www.pnas.org
October 7, 2025 at 6:36 PM
Reposted by Samir Giri
cp-cell.bsky.social
Now online! A chemical radar allows bacteria to detect and kill predators
A chemical radar allows bacteria to detect and kill predators
Pseudomonas syringae can detect and kill microbial predators via a chemical radar (Cra), which also allows the bacterium to infect plants despite predation pressure.
dlvr.it
April 2, 2025 at 2:59 PM
Reposted by Samir Giri
natmicrobiol.nature.com
#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...
How nutrient starvation impacts the gut microbiome - Nature Microbiology
In this 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.
www.nature.com
October 1, 2025 at 5:56 PM
Reposted by Samir Giri
juliusbrennecke.bsky.social
The 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
October 5, 2025 at 9:35 AM
Reposted by Samir Giri
craigmaclean.bsky.social
New 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...
Evolutionary rescue accelerates competitive exclusion in a parasite community
Environmental stress drives biodiversity loss by altering competitive hierarchies and pushing taxa towards extinction. Parasites and their communities are particularly vulnerable to stress due to envi...
www.biorxiv.org
September 29, 2025 at 1:54 PM
Reposted by Samir Giri
paulbrainey.bsky.social
A 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.
pnas.org Proceedings of the National Academy of Sciences @pnas.org · Sep 23
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
An illustration of a human and a robot watering a tree together. Image credit: Dave Cutler (artist).
September 23, 2025 at 8:12 PM
Reposted by Samir Giri
evolvedbiofilm.bsky.social
Cool 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/...
September 25, 2025 at 6:29 PM
Reposted by Samir Giri
zaminiqbal.bsky.social
Delighted 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
September 25, 2025 at 9:29 PM
Reposted by Samir Giri
halllab.bsky.social
Excited 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
September 11, 2025 at 2:49 PM