Mizrahi Lab

Final presentations in our Microbial Ecology: Theories & Contemporary Questions course 🎓🦠
Tomer chose to manifest ecological dynamics using visual props.
I love it when people, especially students, color outside the lines.

#ISM2025 Was very fruitful! It was fun to connect with friends and exchange amazing scientific ideas.
Also, we had the chance to present our work!
Our postdoc, Omer Lavy, shared his research on "biblical poop."
Our PhD student, Sarah Winkler, presented her poster on "Decoding Microbial Communities"

Intraspecies warfare restricts strain coexistence in human skin microbiomes - Nature Microbiology About 15,000 pairwise interactions within S. epidermidis from 18 people in 6 families reveal the antagonism and molecular trade-offs that shape the skin microbiota.

Engrafting a new microbe into an ecosystem remains a challenge. ⛰️ New article profiles ~15K interactions between S. epidermidis strains, showing a direct antagonism between strains - as a major barrier to coexistence.
Nice work!
@contaminatedsci.bsky.social @mancusosci.bsky.social

shorturl.at/XTvfC

What a strike! 🎳 Our lab's bowling event was a blast! So much fun hitting the lanes and making memories with the team.

#LabLife #Bowling #TeamFun #ScienceSquad

Great job, Asaf and team! Really interesting findings.

We have a new 3-year postdoc position in our group at the @hifmb.de to study plasmids and plasmids systems of the marine environment to survey their utility in microbial responses to environmental change.

Please see the official job ad here, and spread the word:

jobs.awi.de/Vacancies/20...

Our Post-doc Omar Tovar rocked it at #INRAE2025! 🎉
He presented his fascinating work on "Exploring the functional patterns of the core rumen microbiome." Huge thanks to @inrae-france.bsky.social ‬for hosting!

Macroecological patterns in experimental microbial communities Author summary Determining whether an empirical pattern can be manipulated is a crucial step towards building a predictive theory. Our study aimed to determine the extent that experimental manipulatio...

Macroecological patterns in experimental microbial communities, led by Will Shoemaker & Jacopo Grilli
journals.plos.org/ploscompbiol...

Love this!

Through the new PLASFIGHTER project, we drive significant advances in unravelling and fighting AMR.
We study plasmid-bacteria interactions to answer important questions about their role in generating and maintaining superbugs.

Discover the project ➡️ plasmidlab.es/project/ 

#AntibioticResistance

HiBC: a publicly available collection of bacterial strains isolated from the human gut Nature Communications - Here, the authors present and characterise a collection of human gut bacteria including novel taxa associated with health conditions and a large diversity of plasmids. All...

Very happy that HiBC is out: rdcu.be/ekSCO 🔥 @natcomms.nature.com Excellent team spirit, and, as always, great driving factor by @tcahitch.bsky.social ⭐⭐⭐⭐ We hope that these bacterial isolates from the human gut will facilitate many studies by others... 😀

Nice work!

Moving from genome-scale to community-scale metabolic models for the human gut microbiome - Nature Microbiology In this Perspective, Deiner, Gibbons and colleagues describe the current strengths and limitations of microbial community-scale metabolic models in microbiome research.

Modeling the microbiome is complex, but metabolic interactions offer a path to better models 🦠 However, Scaling from singles to communities is still a challenge. Check this new paper about the Hits & Misses of community-scale metabolic models - rdcu.be/ehkVn
@gibbological.bsky.social @cdiener.com

Microbiomes are vital for, well, everything. We're finally getting serious about cultivating them! Big implications for biotech, medicine, etc. Time to get our hands dirty (in a good way!)

Early Birds get the best deal! 🐦✨

Are you passionate about evolutionary biology? Don’t miss the chance to register for ESEB 2025 at the exclusive Early Bird rate! 
Secure your spot 👉🏻https://eseb2025.com/registration/

The South American MicroBiome Archive (saMBA): Enriching the healthy microbiome concept by evaluating uniqueness and biodiversity of neglected populations The composition and function of the human gut microbiome has been linked to multiple health outcomes across all world regions, often with region-specific associations. Unfortunately, the extent to whi...

Another step for microbiome research!🔬 New study introduces saMBA, a gut microbiome archive from South America. Understanding the full picture of gut microbiome biodiversity is crucial & saMBA is helping us get there!
@bvalderrama.bsky.social @jfcryan.bsky.social

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

Huge thanks to our team and collaborators—@bwmr.bsky.social, Sarah Morais and all co-authors who made this work possible.

• Structural resolution of key components and biochemical analyses showing complementarity among enzymes driving synergistic activity
• Dual regulation of amylosome function via spatial constraints and expression-level tuning

Our findings include:
• Nanoscale visualization of the amylosome as a dense, cell-bound layer targeting starch granules
• Dynamic protein expression reshaping amylosome enzyme composition in response to different substrates

We used cryo-ET, proteomics, structural biology, and biochemistry to uncover how R. bromii physiology and the architecture of the amylosome complex fine-tune enzyme structure and function to enable resistant starch degradation

R. bromii is a keystone gut microbe that enables resistant starch breakdown in the colon via the amylosome, a dense, cell-bound enzymatic complex. Yet how this machinery enables efficient fiber utilization has remained unclear.

Our new preprint, "Spatial constraints drive amylosome-mediated resistant starch degradation by Ruminococcus bromii in the human colon" is now on bioRxiv! Key findings in the thread below belowhttps://www.biorxiv.org/content/10.1101/2025.03.31.646359v1.full.pdf.

The context of protein expression is absolutely critical – it fundamentally changes how we understand our data, and we need to prioritize it.
Nice work, @tcahitch.bsky.social & @tclavel.bsky.social

Accessory Genomes and Evolutionary Strategies of Antibiotic-Resistant Bacteria at University of Southampton on FindAPhD.com PhD Project - Accessory Genomes and Evolutionary Strategies of Antibiotic-Resistant Bacteria at University of Southampton, listed on FindAPhD.com

Another PhD opportunity to join the growing Microbiology community in Southampton 💪 🦠 🔬
Interested in how bacteria adapt to challenges like temperature changes and antibiotics? Join my lab at UoS to explore the role of accessory elements!
tinyurl.com/PhDbacteriaUoS
Apply here: tinyurl.com/MicroUoS

Assessing toxicity and competitive fitness of Vibrio isolates from coastal waters in Israel | mSphere The ocean’s surface water temperatures have increased in the past decades due to climate change. This increase correlates with the spread of Vibrio, a genus of aquatic bacteria, many of which are pathogens of humans and marine animals. Since Vibrio-...

Our paper on vibrios isolated from Israel's coastal waters is now online in mSphere (now with a working link). We analyzed the pathogenic potential (genome sequences, toxicity, and antibiotic resistance) of 23 new isolates.
🦠
#T6SS #T3SS #MARTX
journals.asm.org/doi/10.1128/...

Here's a picture taken in our lab of our staff scientist Sarah Morais working in our anaerobic lab. A truly "one picture worth a thousand words" moment! ✨

Adaptation of the Gut Microbiota to Modern Dietary Sugars and Sweeteners The consumption of sugar has become central to the Western diet. Cost and health concerns associated with sucrose spurred the development and consumpt…

Greatly enjoyed this thought provoking, deeply researched, and extremely well written review from @saradirienzi.bsky.social and Robert Britton

www.sciencedirect.com/science/arti...

ERC-funded PhD (infection biology) and a Postdoc (genetic engineering) position in my lab. #phagetherapy

Do not miss the opportunity to network and participate in FAIR microbiome science 😄 Upcoming @nfdi4microbiota.bsky.social event, May 19-20. Keynote by Prof. John Penders (www.maastrichtuniversity.nl/j-penders/re...)

I am excited to share our latest study, led by Svetlana Volotsky, reveals that archerfish can categorize objects using a small population of neurons in their optic tectum—an early visual processing stage www.nature.com/articles/s41.... (1/4)