Pamela Ferretti

⚠️ Be aware! There are phishing websites for commonly used bioinformatics tools! ⚠️ Samtools and minimap2 affected, but it's likely just the tip of the iceberg. Be careful to use only official sources for your downloads, and let your colleagues and lab members know.
#bioinformatics #microsky

Are you a scientist who speaks Italian? Consider joining this initiative that connects scientists with elementary or middle school students in Italy through monthly correspondence ✒️

If you generate or reuse #microbiome data, check out these guidelines for equitable sequence data reuse. Grateful to @alexjprobst.bsky.social and his team for leading this important work and for bringing together 160+ microbiome scientists (myself included) to contribute!

doi.org/10.1038/s415...

A roadmap for equitable reuse of public microbiome data - Nature Microbiology In this Consensus Statement, a consortium of microbiome scientists discuss current sequencing data sharing policies and propose the use of a Data Reuse Information (DRI) tag to promote equitable and collaborative data sharing.

Our article on equitable reuse of public sequencing data is out! Led by @alexjprobst.bsky.social, @lhug.bsky.social, Cristina Moraru, @geomicrosoares.bsky.social, @folker.bsky.social and myself -, co-authored by Anke Heyder, and developed in consultation with 167 scientists. tinyurl.com/n6yeanmk

A hidden confounder for microbiome studies: medications used years before sample collection | mSystems This is the first study using detailed retrospective medication usage data from electronic health records to systematically assess the long-term effects of medication usage on the gut microbiome. We identified carryover and additive effects on the gut microbiome for a range of antibiotics and non-antibiotic medications, such as benzodiazepine derivatives, antidepressants and glucocorticoids, among others. These findings highlight a collateral effect of diverse drug classes on the gut microbiome, which warrants accounting for long-term medication usage history when assessing disease-microbiome associations.

Here the original article:
@oliveraasmets.bsky.social
@tartumicrobiome.bsky.social @elinorg.bsky.social @estbiobank.bsky.social

doi.org/10.1128/msys...

The gut remembers: the long-lasting effect of medication use on the gut microbiome | mSystems Over the past decades, medication use has steadily increased worldwide, with individuals frequently taking multiple medications (polypharmacy), often repeatedly over extended periods of time (1). Yet,...

My commentary article, featuring the work of Aasmets et al. on the long-lasting effects of medications on the gut microbiome, is now out in mSystems @asm.org
#microbiome #microsky

doi.org/10.1128/msys...

Full thread will come later, but @annacusco.bsky.social's preprint on the dog pet gut microbiome is out!

Using ONT+Illumina, we get better MAGs than to corresponding species representative in public databases

doi.org/10.1101/2025...

Frontiers | Day/night fluctuations of breast milk bioactive factors and microbiome IntroductionHuman breast milk is a sophisticated and complex biological fluid that provides crucial nutritional, immunological, and microbial benefits to inf...

DYK that mothers' milk has a circadian rhythm, providing dynamic signals to baby? 🤱🏻🕧🕐

New study shows:
- Cortisol peaks in early am ('wake up!' 😀)
- Melatonin peaks late at night ('sleepy time' 😴)

Moms who pump may want to label & feed am/pm milk separately.

www.frontiersin.org/journals/nut...

Really timely and important work to tackle global #honeybee population decline: 🐝

Engineered yeast provides rare but essential pollen sterols for honeybees
www.nature.com/articles/s41...

@philstevenson.bsky.social

Kudos to @biocs.bsky.social, @tsbschm.bsky.social and the entire @borklab.bsky.social for tackling over 2000 Git issues to build this database!

Check out @biocs.bsky.social's thread for more details:

bsky.app/profile/bioc...

Whether you're looking to conduct a #microbiome meta-analysis or exploring the database for your next study design, the Metalog database will hopefully save you weeks (or even months) of work!

metalog.embl.de

Manually curated and harmonized metadata for over 110k metagenomic samples! (58k samples from the human gut alone!)🦠

Proud to have contributed to Metalog, the latest @borklab.bsky.social resource:

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

#microsky #microbiome

Metalog: curated and harmonised contextual data for global metagenomics samples Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals and the environment. While sequencing data is deposited in public databases, the associated context...

We hope many of you will find it useful, and will continue to add data. Here's the preprint: www.biorxiv.org/content/10.1... - hopefully coming soon to a NAR Database Issue near you 😅 Thanks to everyone in the @borklab.bsky.social @embl.org who contributed to this! 7/7

We're very happy to release our new database Metalog metalog.embl.de ! It offers manually curated and harmonised contextual data for 110k metagenomics samples across the globe, incl. precomputed taxonomic profiles, for interactive browsing and for download 🧵 1/7

#microsky

Added!

Hi Melissah, this is a really interesting project! Since it involves wild animals, can I add you to the "wild animal microbiome" starter pack here on Bluesky?
go.bsky.app/LXjWaJq

Sure, added!

Certainly! Added!

Done! 👍

Can I add you to the "wild animal microbiome" starter pack here on Bluesky? Your topic of research is a perfect fit

go.bsky.app/LXjWaJq

Please seek the advice of a wildlife rehabilitator. If a hedgehog is out during the day, it's a sign it's extremely sick (last resort attempt to keep their body warm).

YouTube video by Lucas Genoma Do hosts really matter for mosquito-born disease transmission? - Kyle Dahlin

Do hosts really matter for mosquito-born disease transmission? by Dr. Kyle Dahlin @kjmd.bsky.social
www.youtube.com/watch?v=2K2_...

Check out the publications from the workshop:

- Theory of host-microbe symbioses: Challenges and opportunities doi.org/10.1016/j.ch...

- Coexistence of bacteria with a competition-colonization tradeoff on a dynamic coral host @theogibbs.bsky.social doi.org/10.1101/2024...

Stay tuned for more!

Kudos to @lucasgenoma.bsky.social for recording, editing, and uploading these videos 🙏

YouTube video by Lucas Genoma Is the holobiont a unit of selection? A mathematical framework - Taom Sakal

- Is the holobiont a unit of selection? A mathematical framework - Dr. Taom Sakal
youtu.be/wVPdwbebJmg
PDF of Thesis: escholarship.org/uc/item/45w1...

YouTube video by Lucas Genoma Tripartite Phage Bacteria Eukaryote Symbioses in Marine Environments - Cynthia Silveira

- Tripartite Phage Bacteria Eukaryote Symbioses in Marine Environments by Prof. @cynthiasilveira.bsky.social
youtu.be/aPi1xDUA4vo

YouTube video by Lucas Genoma The Hologenomic Origin of Speciation - Dr. Seth Bordenstein

- The Hologenomic Origin of Speciation by Prof. @symbionticism.bsky.social
youtu.be/aggLCHG2Bb4

YouTube video by Lucas Genoma Eco-evolutionary dynamics on coral reef networks - Dr. Lisa C. McManus

- Eco-evolutionary dynamics on coral reef networks by Prof. @lisamcmanus.bsky.social
youtu.be/znNnjaEYMH0

- Lytic/Lysogenic Transition as a Life History Switch by Prof. Joan Roughgarden
lnkd.in/gGJ9r4ss
PDF of presentation: lnkd.in/g3cadFDy

Last year, I joined a brilliant group of researchers for a 3-week deep dive into host–microbe systems. Each week explored a different theme, led by inspiring lecturers.

I’m excited to share that videos of their talks — along with presentations by several team members — are now on YouTube: