Welcome!

me.jpg

Pamela Ferretti

I’m a postdoctoral scholar in the Laboratory of Prof. Ran Blekhman at the University of Chicago, where I study how the microbiome impacts health through metagenomic and genomic approaches. I am interested in understunding how the interplay between microbiome, diet, and social interactions impacts health outcomes and development in early life. In particular, my current projects are focused on:

  • Investigating the role of maternal breast milk in modulating infant health leveraging multi-omics data. Breast milk is often an infant’s sole source of nutrition during the first months of life, yet its microbial and molecular composition, and how these components influence the developing gut microbiome and infant health, remain poorly understood. My recent work, showed that microbes in breast milk help shape the development of the infant gut microbiome. I am now expanding this research to understand how other components of breast milk influence infant health. This project is in collaboration with Prof. Ellen Demerath at the University of Minnesota.

  • Investigating the transmission of the microbiome and antimicrobial resistance genes within hospitals. Hospitals represent a hotspot for the development of antimicrobial resistance and the acquisition of pathobionts during hospitalization can have serious health consequences, especially for vulnerable patients. I’m investigating how infants in the Neonatal Intensive Care Unit (NICU) acquire microbes and antimicrobial resistance genes, and the factors that shape this process. This project is in collaboration with the SET Center at the University of Chicago.

I also study the role of the microbiome in the health of wild animal populations, including baboons in the Amboseli Ecosystem (Kenya), rock hyraxes in Ein Gedi(Israel) and wolves. I’m particularly interested in how the microbiome is transmitted between individuals within social groups, and how its composition affects offspring survival, long-term health, and aging.

Most Recent News

An overview of all news can be found here.
Dec 15, 2025 Our review is now featured in the January issue of Nature Reviews Genetics.
Dec 7, 2025 The interview on my international experience as researcher has been published on the Italian newspaper Gazzetta dell’Emilia.
Oct 29, 2025 Our preprint on milk and infant gut microbiome has been updated with new analysis and results! Stay tuned for more details.
Oct 8, 2025 New preprint out on the demographic, behavioral, and ecological data from the Amboseli Baboon Research Project, one of the longest-running studies of a wild mammal population in the world
Sep 26, 2025 New guidelines for equitable sequence data reuse are now published in Nature Microbiology. Grateful to Prof. Alex Probst and his team for leading this important work and for bringing together 160+ microbiome scientists (myself included) to contribute.

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, Marco Rossi, Timothy Heisel, Sara Gonia, Dan Knights, David Fields, Frank Albert, Ellen Demerath, Cheryl Gale, and Ran Blekhman
    Nature communications, 2025
  2. Theory of host-microbe symbioses: challenges and opportunities
    Pamela Ferretti, Maria Martignoni, Lisa McManus, Taom Sakal, Armun Liaghat, Bethany Stevens, Kyle Dahlin, Lucas Souza, Zoe Cardon, Cynthia Silveira, Seth Bordenstein, and Joan Roughgarden
    Cell Host & Microbe, 2025
  3. Genomics of host–microbiome interactions in humans
    Pamela Ferretti, Kelsey Johnson, Sambhawa Priya, and Ran Blekhman
    Nature Reviews Genetics, 2025
  4. 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
  5. 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
  6. Diversity within species: interpreting strains in microbiomes
    Thea Van Rossum*, Pamela Ferretti*, M. Oleksandr Maistrenko*, and Peer Bork
    Nature Reviews Microbiology, 2020
  7. 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