Pamela Ferretti
@pamferretti.bsky.social
Postdoc in the Blekhman lab at UChicago | Infant and breast milk microbiome | wild animal microbiome | antimicrobial resistance | microbial ecology | Member of @microbiomevif.bsky.social https://pamelaferretti.net/
I did an interview on the MVIF podcast with @pamferretti.bsky.social about wild animal microbiomes, for anyone interested! 🦠🧬
Microbiome Virtual International Forum@microbiomevif.bsky.social · last mo.#MVIFconversations podcast episode 6 with @elinvidevall.bsky.social is OUT! ▶️ Spotify: open.spotify.com/episode/39MK... ▶️ Amazon music: music.amazon.com/podcasts/81c... ▶️ Apple Music: podcasts.apple.com/us/podcast/e... ▶️ YouTube podcast: youtu.be/_wQ4AxWoPTc 1/2
Interested in wildlife microbiomes? Check out the latest @microbiomevif.bsky.social podcast episode, where @elinvidevall.bsky.social explains how the #microbiome influences health and survival in wild animal populations, and why microbes matter for #wildlife conservation efforts! 🧪🦒🦌
Microbiome Virtual International Forum@microbiomevif.bsky.social · last mo.#MVIFconversations podcast episode 6 with @elinvidevall.bsky.social is OUT! ▶️ Spotify: open.spotify.com/episode/39MK... ▶️ Amazon music: music.amazon.com/podcasts/81c... ▶️ Apple Music: podcasts.apple.com/us/podcast/e... ▶️ YouTube podcast: youtu.be/_wQ4AxWoPTc 1/2
Our host @pamferretti.bsky.social & @elinvidevall.bsky.social discuss - how early-life microbial exposure can shape growth &survival, - why captivity can dramatically alter animal microbiomes, and - how microbes may represent a missing piece in wildlife conservation. Click PLAY to hear more! 2/2
The last 10 days have been incredibly exciting and tremendously helpful to understand #baboon diet and behavior in the wild. Day after day, I have watched them navigate the complex social hierarchies within their groups while spending most of their time grooming and foraging.
Thrilled to share that I'll soon be at the Amboseli National Park in Kenya to do exciting field work with the @archielab.bsky.social. Huge thanks for this opportunity to the ISME Mobility Fund, which funded the trip. ✈️
Excited to share that earlier this spring, I received one of the Best Poster Presentation Awards at the Human Milk Institute Symposium in San Diego. Thanks to the organizers Lars Bode @drlarsbode.bsky.social and Mitra Hooshmand for the award and for hosting such a wonderful event!
How well do ARG detection pipelines agree when applied to the same data? Spoiler: not very well. In our new preprint, we ran 10 pipelines on 270M microbial unigenes from GMGCv1. The same data can support conflicting biological conclusions! 🧵 www.biorxiv.org/content/10.6...
The elusive resistome: a global comparison reveals large discrepancies among detection pipelines
Identifying antibiotic resistance genes (ARGs) from metagenomic data is critical for studying antimicrobial resistance across microbial communities and pathogens. However, there is no standardized methodology for ARG annotation. Here, we compare ten commonly used ARG detection pipelines by analysing over 270 million prokaryotic genes from the Global Microbial Gene Catalogue across 13 distinct habitats. We observed up to a 45-fold difference in the number of reported ARGs, with a mean Jaccard index of only 16% between pipelines. Pipeline selection profoundly impacted downstream biological interpretations, with drastic changes to estimates of ARG relative abundance and richness, to the characterization of pan- and core-resistomes, and to the class-level composition of the inferred resistome. ARG detection pipelines make different, defensible trade-offs, and no single approach should be treated as authoritative. Therefore, users should justify and communicate choices carefully, as our analyses show that, taken uncritically, the same data can support conflicting biological and ecological interpretations. ### Competing Interest Statement The authors have declared no competing interest. National Health and Medical Research Council of Australia (NHMRC), 2031902 Australian Research Council (ARC), FT230100724 International Development Research Centre (IDRC), 109304-001 Deutsche Forschungsgemeinschaft (DFG), FO1279/6-1 Bundesministerium für Bildung und Forschung (BMBF), F01KI1909A, 01KI2404B Swedish Research Council (VR), 2024-06123, 2019-00299, 2023-01721 Knut and Alice Wallenberg Foundation, KAW 2020.0239 Swedish Foundation for Strategic Research, FFL21-0174
biorxiv.org
You missed the last #MVIF... No problem, now you can enjoy reading #MVIF 48 reflections! @memartino.bsky.social (ATL) & @kate-lagerstrom.bsky.social (PAC) opened the event w/highlights: @pamferretti.bsky.social talked abt how breast milk directly seeds & stabilizes the infant gut microbiome, 1/n
Science outreach today in middle school classes: we extracted DNA from strawberries🍓 One kid while staring at the clumped pink DNA in her vial shouted "that's so sigma!" Turns out all that time spent watching brainrot videos shared by friends was useful after all!
#MVIF 48 starts next week! Free registration: cassyni.com/s/mvif-48 ⭐️ Highlights: 🇺🇸 Rachel R. Rock 🇺🇸 @pamferretti.bsky.social ⭐️ Keynote: 🇦🇺 @pam-engelberts.bsky.social and @jamesvolmer.bsky.social ⭐️ Talks: 🇨🇳 Linxing Chen 🇨🇳 Zhemin Zhou 🇦🇺 Hoai-An Nguyen
We have a new #MVIF program to share with you! 🤩 Free registration: cassyni.com/s/mvif-48 ⭐️ Highlights: 🇺🇸 Rachel R. Rock 🇺🇸 @pamferretti.bsky.social ⭐️ Keynote: 🇦🇺 Gene Tyson ⭐️ Talks: 🇨🇳 Linxing Chen 🇨🇳 Zhemin Zhou 🇦🇺 Hoai-An Nguyen
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/...
26w5607: New Mathematical Theory in Eco-Evolutionary Modelling of Host-Symbiont Communities | Banff International Research Station
Workshop at the Banff International Research Station in Banff, Alberta between Feb 8 and Feb 13, 2026: New Mathematical Theory in Eco-Evolutionary Modelling of Host-Symbiont Communities.
birs.ca
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
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
nature.com
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
Our Review article is now featured in the January issue of @natrevgenet.nature.com, check it out!
Nature Reviews Genetics@natrevgenet.nature.com · 8mo agoReview: Genomics of host–microbiome interactions in humans by @pamferretti.bsky.social ocial, Kelsey Johnson, @sambhawa.bsky.social & @blekhman.bsky.social rdcu.be/etIRy
📢 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
James Bonfield@jbonfield.bsky.social · 11mo agoHeads 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
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 ✒️
Penne Amiche della Scienza@penneamiche.bsky.social · 11mo ago🚨 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
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.
doi.org
Alex Probst@alexjprobst.bsky.social · 10mo agoNew article on equitable reuse of public sequencing data, published in @natmicrobiol.nature.com! Led by the Data reuse core team @lhug.bsky.social @environmicrobio.bsky.social Cristina Moraru, @geomicrosoares.bsky.social, @folker.bsky.social and with Anke Heyer and The Data Reuse Consotrium!
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
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
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...
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...
frontiersin.org
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
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
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
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...
biorxiv.org
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
Metalog
Metalog is a repository of manually annotated metadata (or contextual data) for metagenomic sequencing data from across the globe.
metalog.embl.de
