Samir Giri

Vaccine-enhanced competition permits rational bacterial strain replacement in the gut Colonization of the intestinal lumen precedes invasive infection for a wide range of enteropathogenic and opportunistic pathogenic bacteria. We show that combining oral vaccination with engineered or ...

Can oral vaccination with competitor bacteria enable pathogen exclusion & strain replacement in gut?
It prevents/displaces pathogens like Salmonella and E. coli in mice, relying on adaptive immunity & niche competition, unveiling a path for microbiota-based therapies www.science.org/doi/10.1126/...

The human skin microbiome: from metagenomes to therapeutics Nature Reviews Microbiology, Published online: 04 August 2025; doi:10.1038/s41579-025-01211-9In this Review, Oh and Voigt explore the major characteristics and functions of the skin microbiome, and they highlight potential therapeutic targets in the skin microbiome and ongoing progress in the development of skin microbiome-based therapeutics.

New online! The human skin microbiome: from metagenomes to therapeutics

Mutualism between degraders and nondegraders stabilizes the function of a natural biopolymer-degrading community | PNAS Natural biopolymer-degrading microbial communities drive carbon biogeochemical cycling. Within these communities, polymer degraders facilitate the ...

Mutualism stabilises biopolymer degradation by expanding ecological niches, limiting resource exploitation through substrate-specific enzymes, enabling cooperative breakdown; & can be used to design efficient synthetic consortia for biopolymer conversion doi.org/10.1073/pnas...

Habitat filtering more than microbiota origin controls microbiome transplant outcomes in soil Abstract. Human activities cause a global loss of soil microbiome diversity and functionality. One way to reverse this trend is through microbiota transpla

Outcome of soil microbiome transplants is controlled more by selective pressures of recipient soil environment (habitat filtering) than original composition of transplanted community, emphasising habitat’s characteristics, not microbiota origin, determine transplant success👇 
doi.org/10.1093/isme...

Ultraprocessed or minimally processed diets following healthy dietary guidelines on weight and cardiometabolic health: a randomized, crossover trial - Nature Medicine A free-living trial in people with overweight or obesity found that minimally processed diets led to greater weight loss and cardiometabolic improvements than ultraprocessed diets following UK healthy...

A randomized trial of ultraprocessed vs minimally processed food diets for 8 weeks
Guess which one led to more weight and fat mass loss
www.nature.com/articles/s41...

Evolution and evolvability of rifampicin resistance across the bacterial tree of life | PNAS Predicting the ability of bacteria to develop antibiotic resistance is challenging, especially for the vast majority of species for which no experi...

Evolution and evolvability of rifampicin resistance across the bacterial tree of life www.pnas.org/doi/abs/10.1... #jcampubs

Mutualism between degraders and nondegraders stabilizes the function of a natural biopolymer-degrading community | PNAS Natural biopolymer-degrading microbial communities drive carbon biogeochemical cycling. Within these communities, polymer degraders facilitate the ...

Mutualism between degraders and nondegraders stabilizes the function of a natural biopolymer-degrading community www.pnas.org/doi/abs/10.1... #jcampubs

A broad-spectrum antibiotic targets multiple-drug-resistant bacteria with dual binding targets and no detectable resistance - Nature Communications Through a synthetic-bioinformatic natural product approach combined with peptide optimization, a nature inspired antibiotic, paenimicin, was identified from Paenibacillaceae family. Paenimicin feature...

Keep an 👁️ on PAENIMICIN

Novel 11-residue depsi-lipopeptide found in synthetic-bioinformatic screen of Paenibacillaceae

Binds phosphate and hydroxyl groups on lipid A in Gram- bacteria and teichoic acids in Gram+ bacteria → broad spectrum activity

in vivo efficacy, favorable PK, no nephrotoxicity

Polypeptides synthesized by common bacteria in the human gut improve rodent metabolism - Nature Microbiology Two polypeptides synthesized by common bacterial strains in human gut microbiota lower body fat and blood glucose and increase bone density, improving the metabolism of rodents.

🦠 ENDOCRINOLOGY?

RORDEP1/2 secreted by gut commensal 𝘙𝘶𝘮𝘪𝘯𝘰𝘤𝘰𝘤𝘤𝘶𝘴 𝘵𝘰𝘳𝘲𝘶𝘦𝘴 mimic exercise hormone irisin → systemic effects on host metabolism

⭡ thermogenesis, insulin signaling, glycolysis

↓ gluconeogenesis, lipogenesis

These peptides may be candidate biologics for obesity and type 2 diabetes

The prototypic crAssphage is a linear phage-plasmid Schmidtke et al. demonstrate that C. communis, a ubiquitous human gut phage that evades conventional plaque-based isolation, predominately replicates as a low-copy linear phage-plasmid with a broad ho...

What is genomic structure & lifecycle of crAssphage & how does it persist & replicate in gut bacteria?
Its a linear DNA element with phage & plasmid features, persisting as infectious virus and stable plasmid form, explaining its abundance & coexistence w/o host integration. doi.org/10.1016/j.ch...

Metagenomic estimation of absolute bacterial biomass in the mammalian gut through host-derived read normalization | mSystems In this study, we asked whether normalization by host reads alone was sufficient to estimate absolute bacterial biomass directly from stool metagenomic data, without the need for synthetic spike-ins, ...

You can get an accurate estimate of total bacterial biomass from stool metagenomes by simply normalizing by host read count, without needing any additional measurements.

Excellent work by UW Master's student Gechlang Tang in @asm.org #mSystems Journal.

journals.asm.org/doi/10.1128/...
🧵

@kaletalab.bsky.social lab metabolic model reveals diminished exchange of nutrients between host and gut microbiome in diabetes with more competition in microbial communities upon elevated glucose ➡️ www.embopress.org/doi/full/10....

Functional replacement of ancestral antibacterial secretion system in a bacterial plant pathogen Nature Ecology & Evolution - The bacterial plant pathogen genus Xanthomonas uses two distinct secretion systems for antibacterial competition. Here the authors show that some Xanthomonas...

Plant pathogen bacterium replaced its ancestral antibacterial secretion system with a new functional one, revealing bacterial adaptability.
This work highlights evolutionary innovation in microbial competition, crucial for understanding pathogen survival and plant disease dynamics.
rdcu.be/eyz8W

Quantifying the varying harvest of fermentation products from the human gut microbiota Fermentation products are the most abundant gut microbial metabolites absorbed by the host, with important dose-dependent consequences for health. In this study, we present a systems-level analysis in...

Brilliant piece of work from Markus Arnoldini and Jonas Cremer into how much your gut bacteria really do for you!

www.cell.com/cell/fulltex...

Activity of GPCR-targeted drugs influenced by human gut microbiota metabolism Nature Chemistry - Gut microbiota play a critical role in drug metabolism. Now, by exploring the human gut microbial metabolism of G-protein-coupled receptor (GPCR)-targeting drugs, uncommon...

Human gut microbiota metabolize many GPCR-targeted drugs, altering their activity and effectiveness.
This work reports the microbiome’s role in drug response variability and emphasizes incorporating gut microbial composition into personalized medicine and drug development strategies.
rdcu.be/eyz6F

Associate or Senior Editor, Nature Biomedical Engineering Job Title: Associate or Senior Editor, Nature Biomedical Engineering Organization: Nature Portfolio Location: New York, Jersey City, Shanghai or Beijing – Hybrid Working Closing date: August 20, 2025 ...

My colleagues at Nature Biomedical Engineering @natbiomedeng.nature.com are hiring an associate or senior editor. Ideal applicant will have expertise in immunology, immunotherapy, or immuno-oncology.

Please feel to ask me questions!

springernature.wd3.myworkdayjobs.com/SpringerNatu...

Group Leader - Genome Biology Unit Are you ready to lead groundbreaking research in Genome Biology? Join us at EMBL! We are seeking a motivated scientist to lead an independent research group addressing exciting and original biological...

To all post-docs: The Genome Biology dept ‪@embl.org
has an Independent faculty position. Fantastic place to set up your lab –great package: core funding, fantastic Ph.D. students, cutting edge core facilities & great colleagues. Closing date Sept 19th
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

Group Leader – Molecular Systems Biology Unit Are you ready to lead groundbreaking research in Molecular Systems Biology? Join us at EMBL! We are seeking a motivated scientist to lead an independent research group, addressing original biological ...

Pitch your visionary research plan and shape the future of molecular systems biology with us!

Apply by 22 Sep 2025.
embl.wd103.myworkdayjobs.com/en-US/EMBL/d...

@embl.org, @EMBLHeidelberg
#systemsbiology #groupLeader #research #molecularBiology

Group Leader – Molecular Systems Biology Unit Are you ready to lead groundbreaking research in Molecular Systems Biology? Join us at EMBL! We are seeking a motivated scientist to lead an independent research group, addressing original biological ...

Ready to lead pioneering research that bridges systems-level investigations of biological systems to molecular mechanism? The EMBL Molecular Systems Biology Unit in Heidelberg is hiring a Group Leader!

Plasmids link antibiotic resistance genes and phage defense systems in E. coli Phage therapy has been proposed as an alternative to antibiotics to treat resistant infections. However, we have a limited understanding of how antibiotic resistance genes (ARGs) associate with bacter...

New pre-print from my lab!
Plasmids link antibiotic resistance and phage defense.

E.coli plasmids are hotspots for both antibiotic resistance and phage defense. Phage therapy has the potential to accidentally select for antibiotic resistance!!!
#microsky#AMR#phage

www.biorxiv.org/content/10.1....

Ingestible optoelectronic capsules enable bidirectional communication with engineered microbes for controllable therapeutic interventions Nature Microbiology - A smartphone-controlled ingestible capsule can have a two-way communication with engineered microbes inside the gut via light-induced signals.

This paper reports development of a swallowable electronic device that communicates directly with engineered bacteria in the gut, allowing for remote triggering or monitoring therapeutic activities, enabling precise, controllable & targeted microbial therapies inside the human body.
rdcu.be/eyfWu

Peptidoglycan–outer membrane attachment generates periplasmic pressure to prevent lysis in Gram-negative bacteria - Nature Microbiology Outer membrane attachment to peptidoglycan enables periplasmic pressure to build up and counter cytoplasmic turgor pressure, preventing lysis during osmotic challenges in Escherichia coli.

#microsky
We challenge the long-standing view that peptidoglycan alone protects cells from bursting.

Our study shows that the periplasm — enclosed by OM–PG connections — acts as a pressure buffer essential for osmoprotection in Gram-negative bacteria.

📄 www.nature.com/articles/s41...

⏰ Abstract deadline for 'The mobile genome' is 29 July!

👉 https://s.embl.org/mge25-01-bl

Join us 4–7 Nov 2025 at EMBL Heidelberg (or online) to explore the impact of TEs across biology. 🧬🔍

⭐🧑🏼‍🔬 24 talks + 15 flash talks from posters – don't miss out!

#EMBOMobileGenome

We are on the lookout for postdocs for two different projects at the intersection of ecology, evolution, and the human microbiome.

See thread for more information and reach out!

📢 We're seeking a postdoc to work on a project funded by HFSP @hfspo.bsky.social at the intersection of bacterial physiology, ecology and evolution. You can find more details about the project, the position, and how to apply here www.dalbellolab.com/hfsp-project! #bacteria #ecosky #MevoSky #microSky

Enterococcus faecalis modulates phase variation in Clostridioides difficile https://www.biorxiv.org/content/10.1101/2025.07.24.666506v1

The geroprotectors trametinib and rapamycin combine additively to extend mouse healthspan and lifespan Nature Aging - Gkioni et al. show that trametinib, which targets the Ras–Mek–Erk pathway, extends lifespan in male and female mice and that co-treatment with the known geroprotector...

Trametinib and rapamycin, targeting MAPK and mTOR pathways respectively, together at low doses, additively extend mouse healthspan and lifespan by ~30%, surpassing the effects of either drug alone and highlighting the potential of combination ageing therapies.

rdcu.be/exHyN

A gut sense for a microbial pattern regulates feeding - Nature A study reveals a gut–brain sensory pathway through which the microbial component flagellin activates neuropod cells in the colon to signal the brain and reduce feeding in mice.

Gut-microbe-brain mechanism controlling feeding behaviour

Specialised colon cells (neuropods) detect bacterial flagellin via TLR5 receptor & quickly signal the brain through vagal nerves to suppress appetite. Disruption of this pathway causes overeating & weight gain in mice.  

rdcu.be/exCl7

This work identifies 'imidazole propionate' as a causal microbial metabolite that promotes atherosclerosis and shows that modulating its levels can potentially prevent cardiovascular disease risk, a promising therapeutic strategy.👇

Imidazole propionate is a driver and therapeutic target in atherosclerosis - Nature Imidazole propionate produced by gut microbiota is associated with atherosclerosis in mouse models and in humans, and causes the development of atherosclerosis through activation of the imidazoline-1 ...

💥 A gut microbe metabolite that drives #atherosclerosis?
Yes—Imidazole propionate (ImP) triggers vascular inflammation without changing cholesterol.
🧪 We show the pathway—and how to block it.
nature.com/articles/s41... #OpenAccess at
@Nature
@CNIC_CARDIO
#CVD #immunosky #cardiosky #microbiomesky