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 in human and wild baboon populations 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, like a mother with her infant or members of a family group. 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.

  • Strain transmission within a population of wild baboons that has been studied for over 50 years, as part of the Amboseli Baboon Research Project. This unique cohort represents the perfect scenario for studying how microbial populations change over time within a social group of hosts. This project is in collaboration with Prof. Elizabeth Archie, Prof. Jenny Tung and members of their research groups.

Most Recent News

An overview of all news can be found at here.
Jan 29, 2024 Our preprint on breastmilk and infant gut microbiome is now online on bioRxiv!
Dec 21, 2023 Our paper, Meconium Microbiome of Very Preterm Infants across Germany, was highlighted as an ASMicrobiology Top Cited paper in 2023
Dec 12, 2023 Launch of this website.
Oct 28, 2023 Our database SPIRE: a Searchable, Planetary-scale mIcrobiome REsource is now published in Nucleic Acids Research.

Selected Publications

  1. Assembly, stability, and dynamics of the infant gut microbiome are linked to bacterial strains and functions in mother’s milk
    Mattea Allert*, Pamela Ferretti*, 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