Pamela Ferretti

It was a pleasure speaking at the "New Mathematical Theory in Eco-Evolutionary Modelling of Host-Symbiont Communities" workshop, held last week at the Banff International Research Station. Looking forward to seeing everyone in person next time!
www.birs.ca/events/2026/...

Congratulations Chan Yeong!

Hi @arsweeny.bsky.social, can I add you to the Wild Animal Microbiome starter pack?
go.bsky.app/LXjWaJq

Microbes in breast milk help populate infant gut microbiomes New study provides one of the most detailed portraits yet of how different combinations of bacteria in human milk contribute to infants’ gut microbiomes.

The press release highlighting the results of our breast milk microbiome study is available on the BSD UChicago news page

biologicalsciences.uchicago.edu/news/microbe...

Written by Grace Niewijk, UChicago.
#Milk #Microbiome #Nutrition #Breastfeeding

These are very exciting times for the field, and hopefully these questions won’t stay open for long!

Study designs so far have lacked the appropriate range of body sites sampled, the necessary sampling frequency, and the sequencing depth needed to address these questions. There is no clear evidence yet for a resident mammary gland microbiome either!

While much discussed, I have not yet seen convincing evidence supporting the existence of an entero-mammary pathway (maternal gut -> milk). Rather, I think gut taxa might end up in breast milk through the infant’s oral cavity shortly after birth (maternal gut -> infant oral cavity -> milk).

Thanks Matt! That's another major open question in the field. Where do these microbes come from? Skin around the nipple and retrograde flow (infant's oral microbiome -> milk) are both very plausible, but some milk taxa are typically found in the gut.

Huge thanks to the team that made this work possible: Mattea Allert, Kelsey Johnson, Marco Rossi, Timothy Heisel, Sara Gonia, Dan Knights, David A. Fields, Frank Albert, Ellen Demerath, Cheryl Gale and @blekhman.bsky.social.

This project would not have been possible without funding from the NIH.

Finally, we explored the antimicrobial resistance genes and functional potential of microbes found in breast milk and in the infant gut. Check out the paper for more results!

Four phylogenetic trees show examples of strain sharing between milk and infant stool samples for specific microbes: B. longum, S. salivarius, P. vulgatus and K. pneumoniae. Instances of mother-infant pairs sharing the same strain are highlighted with black rectangles.

Beyond milk composition, we assessed potential mother-to-infant microbial transmission through breastfeeding. We found that microbes present in both breast milk and the infant gut included not only commensals such as Bifidobacteria, but also potential pathobionts like Klebsiella pneumoniae.

We discuss the possible reasons for this discrepancy and its implications in the paper. TL;DR: a priority for the field is to compare amplicon vs. metaG sequencing of human milk samples to assess the impact of technical factors, such as amplification biases in amplicon sequencing and lysis duration.

Heatmap showing which microbes are present in human milk samples and at what abundance. Bifidobacterium longum is the first of the list.

In contrast to previous amplicon studies that reported the milk microbiome to be dominated by Staphylococcus and Streptococcus, we found that the most prevalent and abundant taxa in milk were #Bifidobacteria. The milk microbiome also included species typically found in the oral cavity, gut, and skin

Excited to share our new study out in Nature Communications. We mapped the composition of the human breast #milk #microbiome and showed that microbes present in breast milk directly contribute to the assembly of the #infant gut microbiome in the first months of life.

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

Breast milk microbes help shape infants' gut microbiomes, study finds Most conversations about breast milk tend to focus on topics like nutrients, antibodies and bonding time rather than bacteria.

Breast milk contains a unique community of microbes that can transfer to infants, influencing the development of the gut microbiome and supporting early immune and metabolic functions. doi.org/hbh4wd

Our Review article is now featured in the January issue of @natrevgenet.nature.com, check it out!

Human figure wrapped in DNA, surrounded by viruses, bacteria, and other microorganisms, with a globe in the background, symbolizing global health and genetics.

📢 Our January issue is live and it's a special one🦠🧫! Featuring a range of article types, including Reviews, Comments and Journal Club articles, this Focus issue explores the insights gained from the application of microbial genomics within ecological and evolutionary contexts go.nature.com/3MNmsgR

🧬 🦠 🏙️
Urban vs rural lifestyles create dramatically different gut microbiomes. But how do these different gut microbiomes affect the host?

Excited to share our new paper: www.biorxiv.org/content/10.1...

⚠️ 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