Ezgi Ozkurt

Really pleased to see this study led by @raymondkiu.bsky.social now published in @natcomms.nature.com!

We show that probiotics help modulate the preterm infant 👶#microbiome - to reduce ARGs, lower MDR bacteria 🦠 & increase beneficial Bifido ✨

Huge team effort!

www.nature.com/articles/s41...

Mechanisms of microbiome assembly and approaches to uncover the ecological forces driving it.

Deriving ecological models solely from observational data limits our ability to understand mechanisms driving microbiome assembly. This #mSystems articles explores how experimental approaches can address these challenges. asm.social/2wj

Experimental systems are essential for strengthening ecological modeling of microbiomes beyond observational data | mSystems Applying community ecology principles to observational microbiome data presents substantial challenges, especially given the complexity of microbial interactions. Even in controlled experiments with only two microbial strains, interactions can be unexpectedly intricate (1, 2), underscoring the difficulty of inferring detailed community dynamics from observational data alone. Additionally, microbiome composition varies widely among individual hosts (3); for instance, only a small fraction of microbial species are consistently shared across human microbiomes (4, 5). This variability arises from factors such as diet (6), genetics (7), geography (8), gender (9), and medication (10), though random events (11) also play a substantial yet often underexplored role. Disentangling the deterministic and stochastic processes driving this variability requires comprehensive metadata collection. However, confounding variables often complicate analysis (12, 13), and it is impossible to fully capture all host-associated factors or confounders without controlled conditions. Consequently, observational (top-down) studies alone offer limited insight into the causes and consequences of microbiome variation. Integrating observational data with controlled (bottom-up) experiments under identical conditions holds great promise for revealing baseline stochasticity and the deterministic factors shaping microbial communities. Understanding these ecological processes in-depth is essential to the success of therapeutic microbiome interventions like fecal microbiota transplantation (FMT) and personalized healthcare, where context-dependent factors and historical contingencies contribute to variable outcomes (14–16). Leveraging these insights enables systematic examination of assembly dynamics, uncovering the ecological principles that govern these complex and variable communities.

Sharing my perspectives on experimental systems & ecological modelling in microbiome research. I’d love to hear your perspectives and have a brainstorming session together. Hope you enjoy the read!

journals.asm.org/doi/10.1128/...

🚨 Aging and Microbiome Conference 2025
📌 Jena, Germany
📆 October 28-29, 2025
⏰ Abstract submission deadline: 31.05.2025
ℹ️ amc25.leibniz-fli.de

Genomes from long-read metagenomic assemblies contain rampant errors, highlighting the pressing need for stricter evaluation methods in long-read assembly algorithms. Read more in our paper with the Eren group. @floriantrigodet.bsky.social @merenbey.bsky.social

Abstract submission for EEBST 2025 has opened 🚨 Submit your abstracts here 👉 eebst.ekoevo.org until May 25th. Looking forward to see you in Ankara!

Core Bioinformatics team at QIB -- job offer to join the team as bioinformatics programmer as per link

Hello binfies 👋!

There is an open position for a senior bioinformatician to join our fab **core bioinformatics** team at @quadraminstitute.bsky.social.

jobs.quadram.ac.uk/Details.asp?...

Mixing microbiomes in vitro reveals rules of community assembly | PNAS Mixing microbiomes in vitro reveals rules of community assembly

Our commentary on the elegant in vitro microbiome coalescence experiments from @goldmandoran.bsky.social @ksxue.bsky.social et al is out.

It was a pleasure to write about one of my favorite microbiome papers of the last few years.

www.pnas.org/doi/10.1073/...

📢 Super excited to announce the Aging and Microbiome Conference 2025 #AMC2025 in Jena, Germany! Join us on October 28–29 for the latest developments and exciting discussions on #microbiome & #aging
📅 Registrations open March 28
🌐 amc25.leibniz-fli.de

Please help us spread the word!

If you generate, or use MAGs, you should really read the work we have done benchmarking their limitations. Using complex mock communities (70 species), we assessed how deeply you need to sequence to accurately conduct common metaG analyses. Webwere shocked to see even HQ MAGs are often chimeric!

Remember, EuropePMC is actually better than #PubMed because it includes ALL preprints in search results, not just those including NIH-funded research.

europepmc.org

IL-17RA signaling provides dual tumor-suppressor function during late-stage colorectal carcinogenesis Members of the interleukin-17 family are associated with tumor progression in various settings. Denk et al. find that, in colorectal cancer, IL-17RA switches from tumor promotion during early tumorige...

Can fungi play a protective role by triggering anti-tumor immunity! Excited to be part of this fascinating study 👇

IL-17RA signaling provides dual tumor-suppressor function during late-stage colorectal carcinogenesis: Immunity www.cell.com/immunity/ful...

A terrific core bioinformatics is looking forward to collaborating with you ⬇️

CroCoDeEL: accurate control-free detection of cross-sample contamination in metagenomic data Metagenomic sequencing provides profound insights into microbial communities, but it is often compromised by technical biases, including cross-sample contamination. This underexplored phenomenon arise...

1/9 🚨 New preprint alert!

Frustrated by strange results with your metagenomic data?

Meet CroCoDeEL, an accurate, easy-to-use tool to detect and quantify cross-sample contamination—no need for negative controls or sample positions!

🔗 doi.org/10.1101/2025...

How to apply

The call for PhD positions at the Max Planck Institute for Evolutionary Biology is now open, including one in my group! www.evolbio.mpg.de/3017297/appl.... If you are interested in playing with ancestral recombination graphs, please reach out!

Host-specific microbiome and genomic signatures in Bifidobacterium reveal co-evolutionary and functional adaptations across diverse animal hosts Animal hosts harbour divergent microbiota, including various Bifidobacterium species and strains, yet their evolutionary relationships, and functional adaptions remain understudied. By integrating tax...

1/ 🚨 New preprint alert! 🚨 We’re thrilled to share our latest work exploring microbiome & genomic #Bifidobacterium co-evolutionary & functional signatures across diverse animal hosts. This has been a long time coming, & huge credit to Magda for her incredible hard work as first author! 🐾✨👇

Ecological dynamics of Enterobacteriaceae in the human gut microbiome across global populations - Nature Microbiology Assessing more than 12,000 metagenomic samples from across the world using computational approaches, the authors determined interactions between species that co-colonize or co-exclude Enterobacteriace...

Delighted to share the first peer-reviewed paper from our team @camvetschool.bsky.social where we investigate the ecological dynamics of Enterobacteriaceae in the human gut #microbiome: www.nature.com/articles/s41... @naturemicrobiol.bsky.social

Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants Preterm infants (<37 weeks’ gestation) are often administered broad-spectrum antibiotics in hospitals due to their vulnerability to severe morbidity, including necrotising enterocolitis and sepsis. Ho...

Starting the new year with a new pre-print from the Hall Lab @halllab.bsky.social looking at the impact of empirical antibiotics on gut microbiome and resistome of both probiotic and non-probiotic supplemented VLBW preterm infants: www.biorxiv.org/content/10.1...
#resistome #amr #microbiome #preterm

By sequencing the microbiome of a highly replicated sample of seeds from the same wheat plant and field, the study provides new insights into the stochastic patterns of seed-associated microbiome composition and transmission in wheat.

Ecological assembly dynamics of the seed-borne microbiome in cultivated and wild wheat Background Plants host diverse microbial communities that can significantly impact plant health. A portion of these communities is vertically transmitted to the next generation through seeds, influenc...

Before taking a break from science for some months, I’m happy to share the final chapter of my PhD thesis, now available as a preprint.
This project holds a special place in my heart as it is the very first one I designed myself.
www.biorxiv.org/content/10.1...

a picture of captain america with the words see you soon ALT: a picture of captain america with the words see you soon

A right before new year classic: Manuscript submitted.
A very different year starts for me now..happy new year 🎄

Researchers describe a novel mechanism that allows Drosophila to combat enteric pathogens while also preserving the beneficial indigenous microbiota.
https://buff.ly/4fgP8HB

deevybee.blogspot.com/2024/12/finl...
re @zbmed.bsky.social new contract

Are @zbmed.bsky.social aware of the negative reaction on social media to their just-announced contract with MDPI. There's a great many red flags they seem to have missed, e.g.
deevybee.blogspot.com/2024/08/gues...
deevybee.blogspot.com/2024/02/the-...
+ @hansonmark@bsky.social's account below

Hi Jan! Would love to be added to this..