Author

P. Ferretti

University of Chicago

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Microbiology· 4

Signature Assays, Organisms & Methods

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Assay:metagenomics· 4 Organism:human· 3 Research Focus:clustering· 2 Approach:statistical model· 2 Research Focus:cell type annotation· 1 Research Focus:cell-cell communication· 1 Research Focus:database / resource· 1 Research Focus:differential expression· 1

Frequent Co-Authors

A. Fullam· 2 shared C. Schudoma· 2 shared M. Kuhn· 2 shared P. Bork· 2 shared T. S. Schmidt· 2 shared A-S. Andrei· 1 shared A. De Santiago· 1 shared A. Krag· 1 shared

Activity by Year

2022-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 23 mutual co-author links

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2 shared papersMicrobiology

A. Fullam

Mutual co-authors in cluster

Author profile →

4 papers

Recent·Most cited

A roadmap for fair reuse of public microbiome data

Laura A. Hug, Roland Hatzenpichler, Cristina Moraru, André Soares, Folker Meyer, Anke Heyder, Rehab Z. Abdallah, Ammar Abdalrahem, Nafi’u Abdulkadir, Ibukun Modupe Adesiyan, Lauren V. Alteio, Karthik Anantharaman, Rika E. Anderson, A-S. Andrei, Juan Antonio Baeza, , Matthew Kellom

The paper proposes a roadmap for fair reuse of public microbiome data by introducing a Data Reuse Information tag (DRI) to facilitate communication between data creators and consumers.

Nature Microbiology · Sep 26, 2025Peer-reviewedMicrobiology

Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations

S. Nishijima, E. Stankevic, O. Aasmets, T. S. Schmidt, N. Nagata, M. I. Keller, P. Ferretti, H. Juel, A. Fullam, C. Schudoma, S. M. Robbani, J. K. Hansen, L. A. Holm, M. Israelsen, R. Schierwagen, , P. Bork

This study shows that fecal microbial load, not disease, is the main driver of gut microbiome changes and identifies it as a major confounder in microbiome studies.

bioRxiv · Mar 18, 2024Microbiology

Assembly of the infant gut microbiome and resistome are linked to bacterial strains in mother's milk

P. Ferretti, M. Allert, K. Johnson, M. Rossi, T. Heisel, S. Gonia, D. Knights, D. A. Fields, F. W. Albert, E. W. Demerath, C. A. Gale, R. Blekhman

This study links the infant gut microbiome and resistome to bacterial strains in mother's milk using metagenomic samples from mother-infant pairs.

bioRxiv · Jan 28, 2024Microbiology

C. difficile may be overdiagnosed in adults and is a prevalent commensal in infants

P. Ferretti, J. Wirbel, O. M. Maistrenko, T. Van Rossum, R. Alves, A. Fullam, W. Akanni, C. Schudoma, A. Schwarz, R. Thielemann, L. Thomas, S. Kandels, R. Hercog, A. Telzerow, I. Letunic, , P. Bork

This study finds that C. difficile is often overdiagnosed in adults and is a common commensal in infants, with distinct microbial associations across age groups.

bioRxiv · Feb 16, 2022 · PreprintMicrobiology