Pamela Ferretti
banner
pamferretti.bsky.social
Pamela Ferretti
@pamferretti.bsky.social
Postdoc in the Blekhman lab at UChicago | Infant and breast milk microbiome | antimicrobial resistance | wild animal microbiome | microbial ecology | MVIF member
https://pamelaferretti.net/
Pinned
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...
Client Challenge
www.nature.com
Congratulations Chan Yeong!
February 9, 2026 at 10:10 PM
Hi @arsweeny.bsky.social, can I add you to the Wild Animal Microbiome starter pack?
go.bsky.app/LXjWaJq
January 14, 2026 at 4:08 PM
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
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.
biologicalsciences.uchicago.edu
January 13, 2026 at 5:52 PM
These are very exciting times for the field, and hopefully these questions won’t stay open for long!
January 9, 2026 at 7:15 PM
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!
January 9, 2026 at 7:15 PM
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).
January 9, 2026 at 7:15 PM
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.
January 9, 2026 at 7:15 PM
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.
January 9, 2026 at 10:28 AM
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!
January 9, 2026 at 10:28 AM
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.
January 9, 2026 at 10:28 AM
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.
January 9, 2026 at 10:28 AM
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
January 9, 2026 at 10:28 AM
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...
Client Challenge
www.nature.com
January 9, 2026 at 10:28 AM
Reposted by Pamela Ferretti
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
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.
medicalxpress.com
January 7, 2026 at 9:20 PM
Our Review article is now featured in the January issue of @natrevgenet.nature.com, check it out!
December 15, 2025 at 9:54 PM
Reposted by Pamela Ferretti
📢 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
December 15, 2025 at 4:59 PM
Reposted by Pamela Ferretti
🧬 🦠 🏙️
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...
November 5, 2025 at 2:04 AM
⚠️ 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
Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.

Ie: it's not us (Samtools team)! Be warned
October 21, 2025 at 2:58 PM
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 ✒️
🚨 Ci manca pochissimo!
Siamo quasi al record di classi coperte… e ci mancano solo pochə scienziatə per arrivarci! 🧪✨
Non perdete l’occasione!
Iscriviti al link → forms.gle/tAWtfxmcJptf...
#PenneAmicheDellaScienza #ScienzaPerTuttə
September 28, 2025 at 1:40 AM
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...
September 26, 2025 at 9:44 PM
Reposted by Pamela Ferretti
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 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.
tinyurl.com
September 26, 2025 at 8:14 PM
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...
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,...
doi.org
September 23, 2025 at 5:33 AM
Reposted by Pamela Ferretti
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...
September 18, 2025 at 12:01 PM
Reposted by Pamela Ferretti
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...
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...
www.frontiersin.org
September 7, 2025 at 11:25 PM