Exciting Senior Scientist 👩‍🔬 👨‍🔬 role available in my research group 🧠 🦠 - Closing date Tuesday 5th August 2025.

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@apcmicrobiomeirel.bsky.social @anatneuroucc.bsky.social
Full details here
my.corehr.com/pls/uccrecru...

Congratulations to all the recipients of the UCC Research & Innovation Awards 2024.

It was an epic evening! Excellent work behind the scenes by the Office of the VP for Research & Innovation team!

#UCCResearchInnovationAwards

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...

Excited to share our preprint on the South American MicroBiome Archive (saMBA)! 🌎🦠.

We analysed one of the regions with the fewest microbiome samples but some of the highest biodiversities.

📄: shorturl.at/Lmvp5
🧵: What did we find—and why? Find out 👇

#microbiome #gut-microbiome
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Brain, bacteria, and behaviour summer course - Understanding the gut brain axis Looking for information about Brain, bacteria, and behaviour summer course? Read more about this Radboudumc agenda item

Registration is open for our summer course on the microbiota gut-brain axis! Learn from experts & gain hands-on analytical experience.

📍 Nijmegen, Netherlands | 📅 7-11 July 2025
Sign up now! 🔗
www.radboudumc.nl/en/agenda/20...

Cheering on @eugenianatasha.bsky.social as she talks about antidepressants and the gut microbiome at Mind Mood Microbes 2025 #MMM25

🚨 PhD Opportunity in Microbiome-Gut-Brain Axis & Bioinformatics! 🚨
Are you passionate about microbiome science, #Bioinformatics, and #Neuroscience? We’re looking for a highly motivated #PhD student to join the #Microbiome-Gut-Brain Axis Research Group with @jfcryan.bsky.social and Ger Clarke

I grew up in Tanzania & strongly believe we rely on nature for our survival…

Yet, over one million species are at risk of extinction due to human activity.

It is time to change. Time to conserve our vital biodiversity & save our degraded ecosystems.

Photo via @UNDESA

📢REGISTRATION NOW OPEN
International Civil Society Conference:
AMBITION & MOMENTUM – FINANCING SUSTAINABLE DEVELOPMENT FOR GLOBAL JUSTICE
Civil Society Recommendations for #FfD4

🌍Online-Event: Feb 19, 2025
12:30PM-4:30PM (CET)
Info & registration: www.globalpolicy.org/en/event/202...

#Fin4Dev #FfD

Fermented foods affect the seasonal stability of gut bacteria in an Indian rural population - Nature Communications Here, the authors profile the gut microbiota and metabolites of Indian agrarians to understand the impact of fermented foods consumption, and identify seasonal variation in the gut microbiota structur...

Fermented foods affect the seasonal stability of gut bacteria in an Indian rural population www.nature.com/articles/s41...

Two decades of bacterial ecology and evolution in a freshwater lake - Nature Microbiology A 471-metagenome time series from Lake Mendota in Wisconsin, USA, reveals seasonal and decadal shifts in bacterial functional and ecological dynamics, especially in response to environmental extremes.

Two decades of bacterial ecology and evolution in a freshwater lake www.nature.com/articles/s41... #jcampubs

Still so proud of bringing #Tolkien to our review and of this wonderful cover!
“Speak Friend and Enter”

MaAsLin 3: Refining and extending generalized multivariable linear models for meta-omic association discovery A key question in microbial community analysis is determining which microbial features are associated with community properties such as environmental or health phenotypes. This statistical task is impeded by characteristics of typical microbial community profiling technologies, including sparsity (which can be either technical or biological) and the compositionality imposed by most nucleotide sequencing approaches. Many models have been proposed that focus on how the relative abundance of a feature (e.g. taxon or pathway) relates to one or more covariates. Few of these, however, simultaneously control false discovery rates, achieve reasonable power, incorporate complex modeling terms such as random effects, and also permit assessment of prevalence (presence/absence) associations and absolute abundance associations (when appropriate measurements are available, e.g. qPCR or spike-ins). Here, we introduce MaAsLin 3 (Microbiome Multivariable Associations with Linear Models), a modeling framework that simultaneously identifies both abundance and prevalence relationships in microbiome studies with modern, potentially complex designs. MaAsLin 3 also newly accounts for compositionality with experimental (spike-ins and total microbial load estimation) or computational techniques, and it expands the space of biological hypotheses that can be tested with inference for new covariate types. On a variety of synthetic and real datasets, MaAsLin 3 outperformed current state-of-the-art differential abundance methods in testing and inferring associations from compositional data. When applied to the Inflammatory Bowel Disease Multi-omics Database, MaAsLin 3 corroborated many previously reported microbial associations with the inflammatory bowel diseases, but notably 77% of associations were with feature prevalence rather than abundance. In summary, MaAsLin 3 enables researchers to identify microbiome associations with higher accuracy and more specific association types, especially in complex datasets with multiple covariates and repeated measures. ### Competing Interest Statement C.H. declares the following associations: Seres Therapeutics (scientific advisory board, microbiome therapies), Microbiome Insights (scientific advisory board, microbiome data generation), Zoe (scientific advisory board), Empress (scientific advisory board, microbiome therapies).

Maaslin3 supports SummarizedExperiment www.biorxiv.org/content/10.1...

TEMPTED: time-informed dimensionality reduction for longitudinal microbiome studies - Genome Biology Longitudinal studies are crucial for understanding complex microbiome dynamics and their link to health. We introduce TEMPoral TEnsor Decomposition (TEMPTED), a time-informed dimensionality reduction ...

New tensor factorization paper out today — a fun collaboration with Pixu Shi, Liat Shenhav, Rob Knight, & Anru_Zhang! 🎉 Check it out here: genomebiology.biomedcentral.com/articles/10....

Sex-specific fear acquisition following early life stress is linked to amygdala and hippocampal purine and glutamate metabolism - Communications Biology This study models early life stress (ELS) to observe sex-specific effects on fear memory formation using innovative unsupervised classification together with cellular metabolism alterations in key str...

We've uncovered sex-specific effects of early-life stress (ELS) exposure on fear memory, HPA-axis regulation, and brain metabolism🧠. Unsupervised clustering shows that fear responses are more than only freezing.
@mathiasvschmidt.bsky.social
nature.com/articles/s42...
Highlights in thread👇

Huge congrats to Dr.Michael Collins who successfully defended his PhD today. Thanks to Examiners Aine Kelly & Olivia O’Leary for great discussions

Also great day for supervisors myself & @kjdoriordan.bsky.social -with his 1st PhD student
@apcmicrobiomeirel.bsky.social @uccresearch.bsky.social

This week I presented my work on the characterization of gut microbiomes across southamerican populations at the annual meeting of the Irish Society of Comp. Bio.

Our work won an award & loads of very good feedback 🥳.

Sadly, I had to crop the pic but (hopefully) we will drop a preprint soon

Extensive impact of non-antibiotic drugs on human gut bacteria Nature - Some non-antibiotic drugs have been associated with changes in gut microbiome composition, but the extent of this phenomenon is unknown. Athanasios Typas and colleagues screened more than...

In a great collaboration with @typaslab.bsky.social, @lisamaierlab.bsky.social and @biocs.bsky.social found that 24% of the tested human-targeted drugs inhibit the growth of gut commensal bacteria.

"Extensive impact of non-antibiotic drugs on human gut bacteria" (2018) www.nature.com/artic...

Some impressive numbers in this thread

Gut physiology and environment explain variations in human gut microbiome composition and metabolism - Nature Microbiology An observational longitudinal clinical trial, incorporating a SmartPill and metabolomics, reveals the role of host factors in shaping the gut microbiome in healthy human adults.

Quite a comprehensive piece of work:

"Gut physiology and environment explain variations in human gut microbiome composition and metabolism."

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

Definitely worth checking out if you work on animal microbiomes, especially in the gut

Some genuinely terrible people whining about the "block culture" here on Bluesky is how you know the block culture is working, keep blocking those genuinely terrible people, folks, soon the only people they'll be able to bother here is each other

I am grateful and honored to have received the APC Microbiome Ireland Future Leaders Award for 2024. It takes a village and I have been fortunate to have a real good one!

@jfcryan.bsky.social
@uccresearch.bsky.social
@ucc.bsky.social

More than just a number: the gut microbiota and brain function across the extremes of life Understanding the interrelationship between the gut microbiota and host physiology, although still in its relative infancy, has taken important steps forward over the past decade. In the context of...

First bluesky post!
I have a new article out www.tandfonline.com/doi/full/10....
First published paper from my post doc at APC Microbiome Ireland @ucc.bsky.social

Microbiome Data Analysis Workshop 2025- UHasselt

Join us for the Microbiome Data Analysis training workshop in Hasselt University (Belgium), December 16-17. More information: www.uhasselt.be/MDAW25

Impacts of maternal microbiota and microbial metabolites on fetal intestine, brain, and placenta - BMC Biology Background The maternal microbiota modulates fetal development, but the mechanisms of these earliest host-microbe interactions are unclear. To investigate the developmental impacts of maternal microbi...

Excellent symposium in Turku BioCity again! Now about the Gut-Brain Axis. Great to meet @biothomaz.bsky.social, @antagomir.bsky.social & co! Presented our research on the impacts of maternal microbiota & microbial metabolites on fetal development. doi.org/10.1186/s129...
#microbiome #MicrobiomeSky

Microbial solutions must be deployed against climate catastrophe

Repeat after me…

@gilbertjacka.bsky.social & colleagues publish same article in 14 different journals in a call to arms to “harness the power of microbiology…. to safeguard the planet for future generations”

Statistical thinking for microbial ecology Most microbial ecologists understand the importance of rigorous statistical analysis for conducting a replicable study. However, formal courses in the statis...

ICYMI, my EMBL seminar was recorded 🙏

It's not a research talk -- it's a mini course on different statistical paradigms and choosing what to estimate in HTS microbiome study.

Check it out! (If you like, no pressure, srsly ❤️)

www.youtube.com/watch?v=VvT3...

When Tolkein meets the microbiota-gut-brain axis....

"Gastrointestinal and brain 🧠 barriers: unlocking gates of communication across the microbiota–gut–brain axis"

Latest review led by fantastic colleague & Middle-Earth aficionado @maburto.bsky.social in Nat Rev Gastro
Read here: rdcu.be/dyDPm

Estimating Fold Changes from Partially Observed Outcomes with Applications in Microbial Metagenomics We consider the problem of estimating fold-changes in the expected value of a multivariate outcome that is observed subject to unknown sample-specific and category-specific perturbations. We are motivated by high-throughput sequencing studies of the abundance of microbial taxa, in which microbes are systematically over- and under-detected relative to their true abundances. Our log-linear model admits a partially identifiable estimand, and we establish full identifiability by imposing interpretable parameter constraints. To reduce bias and guarantee the existence of parameter estimates in the presence of sparse observations, we apply an asymptotically negligible and constraint-invariant penalty to our estimating function. We develop a fast coordinate descent algorithm for estimation, and an augmented Lagrangian algorithm for estimation under null hypotheses. We construct a model-robust score test, and demonstrate valid inference even for small sample sizes and violated distributional assumptions. The flexibility of the approach and comparisons to related methods are illustrated via a meta-analysis of microbial associations with colorectal cancer.

radEmu is here! ❤️🐦📈🔥

The StatDivLab's best differential abundance method yet!

arxiv.org/abs/2402.05231

When stress goes viral...
Delighted to have this collaboration with Colin Hill's lab out in Nature Microbiology. Led by PhD student Nate Ritz we show that the gut virome plays a key role in the modulation of the microbiota–gut–brain axis during stress rdcu.be/dxP4s