Welcome!

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Pamela Ferretti

I’m a postdoctoral scholar in the Laboratory of Prof. Ran Blekhman at the University of Chicago, where I study microbial transmission through metagenomic and genomic approaches. I am interested in studying how commensal as well as pathogenic bacteria spread and persist in individuals that are in close social contact. In particular, my current projects are focused on:

  • Investigating strain transmission between maternal breast milk and her infant’s gut microbiome. The maternal milk often represents the sole source of nutrition for the baby for the first months of life, and yet very little is known about its microbial composition at the species and strain level. This study aims at studying the maternal milk microbiome in relation to the infant’s gut microbiome, and to better represent maternal milk in public repositoriese. This project is in collaboration with Prof. Cheryl Gale and Prof. Ellen Demerath.

  • Investigating microbiome and antimicrobial resistance genes transmission in the hospital context. Hospitals represent a hotspot for the development of antimicrobial resistance and the acquisition of pathobionts during hospitalization can have serious health consequences. This project is in collaboration with the SET Center at the University of Chicago.

In addition, I’m involved in projects studying strain transmission within social groups of wild animals, in particular of wild baboons. This project is part of the Amboseli Baboon Research Project and it is a collaboration with the labs of Prof. Elizabeth Archie and Prof. Jenny Tung.

Most Recent News

An overview of all news can be found here.
Dec 18, 2024 Check out our new preprint on Eukaryotic composition across seasons and social groups in the gut microbiota of wild baboons led by Mary Chege
Nov 15, 2024 Very excited to see this paper finally out in Cell: Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations
Nov 2, 2024 Great experience attending CSHL Microbiome! I presented our work on milk and infant gut microbiome, and the talented student Mary Chege presented our work on the eukaryotes in the gut of wild baboons.
Mar 25, 2024 Our preprint Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations led by Suguru Nishijima is out on bioRxiv! Check it out!
Mar 17, 2024 Excited to have been selected among the 12 participants for the 3 weeks-long workshop on Theory of Microbial Symbiosis at the Hawai`i Institute of Marine Biology

Selected Publications

  1. Assembly, stability, and dynamics of the infant gut microbiome are linked to bacterial strains and functions in mother’s milk
    Pamela Ferretti*, Mattea Allert*, Kelsey Johnson, Timothy Heisel, Sara Gonia, Dan Knights, David Fields, Frank Albert, Ellen Demerath, Cheryl Gale, and Ran Blekhman
    bioRxiv, 2024
  2. SPIRE: a Searchable, Planetary-scale mIcrobiome REsource
    Thomas SB Schmidt*, Anthony Fullam*, Pamela Ferretti, Askarbek Orakov, Oleksandr Maistrenko, Hans-Joachim Ruscheweyh, Ivica Letunic, Yiqian Duan, Thea Van Rossum, Shinichi Sunagawa, Daniel Mende, Robert Finn, Michael Kuhn, Luis Pedro Coelho, and Peer Bork
    Nucleic Acids Research, 2023
  3. C. difficile may be overdiagnosed in adults and is a prevalent commensal in infants
    Pamela Ferretti, Jakob Wirbel*, Oleksandr M Maistrenko*, Thea Van Rossum*, Renato Alves, Anthony Fullam, Wasiu Akanni, Christian Schudoma, Anna Schwarz, Roman Thielemann, Leonie Thomas, Stefanie Kandels, Rajna Hercog, Anja Telzerow, Ivica Letunic, Michael Kuhn, Georg Zeller, Thomas SB Schmidt, and Peer Bork
    eLife, 2023
  4. Meconium microbiome of very preterm infants across Germany
    Jonas Klopp, Pamela Ferretti, Claudius U Meyer, Katja Hilbert, Annette Haiß, Janina Marißen, Philipp Henneke, Hannes Hudalla, Sabine Pirr, Dorothee Viemann, Michael Zemlin, Sofia Kirke Forslund, Christoph Härtel, Peer Bork, Stephan Gehring, Thea Van Rossum, and PRIMAL Consortium
    MSphere, 2022
  5. Diversity within species: interpreting strains in microbiomes
    Thea Van Rossum*, Pamela Ferretti*, M. Oleksandr Maistrenko*, and Peer Bork
    Nature Reviews Microbiology, 2020
  6. Mother-to-infant microbial transmission from different body sites shapes the developing infant gut microbiome
    Pamela Ferretti, Edoardo Pasolli, Adrian Tett, Francesco Asnicar, Valentina Gorfer, Sabina Fedi, Federica Armanini, Duy Tin Truong, Serena Manara, Moreno Zolfo, and  others
    Cell host & microbe, 2018