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/
https://pamelaferretti.net/
Congratulations Chan Yeong!
February 9, 2026 at 10:10 PM
Congratulations Chan Yeong!
Hi @arsweeny.bsky.social, can I add you to the Wild Animal Microbiome starter pack?
go.bsky.app/LXjWaJq
go.bsky.app/LXjWaJq
January 14, 2026 at 4:08 PM
Hi @arsweeny.bsky.social, can I add you to the Wild Animal Microbiome starter pack?
go.bsky.app/LXjWaJq
go.bsky.app/LXjWaJq
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
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!
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!
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
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.
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.
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.
This project would not have been possible without funding from the NIH.
January 9, 2026 at 10:28 AM
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.
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!
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!
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
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.
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.
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
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
Here the original article:
@oliveraasmets.bsky.social
@tartumicrobiome.bsky.social @elinorg.bsky.social @estbiobank.bsky.social
doi.org/10.1128/msys...
@oliveraasmets.bsky.social
@tartumicrobiome.bsky.social @elinorg.bsky.social @estbiobank.bsky.social
doi.org/10.1128/msys...
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.
doi.org
September 23, 2025 at 5:33 AM
Here the original article:
@oliveraasmets.bsky.social
@tartumicrobiome.bsky.social @elinorg.bsky.social @estbiobank.bsky.social
doi.org/10.1128/msys...
@oliveraasmets.bsky.social
@tartumicrobiome.bsky.social @elinorg.bsky.social @estbiobank.bsky.social
doi.org/10.1128/msys...