@article{Nishijima2024,title={Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations},author={Nishijima, Suguru and Stankevic, Evelina and Aasmets, Oliver and Schmidt, Thomas S.B. and Nagata, Naoyoshi and Keller, Marisa Isabell and Ferretti, Pamela and Juel, Helene Bæk and Fullam, Anthony and Robbani, Shahriyar Mahdi and Schudoma, Christian and Kragh Hansen, Johanne and Aas Holm, Louise and Israelsen, Mads and Schierwagen, Robert and Torp, Nikolaj and Arumugam, Manimozhiyan and Bendtsen, Flemming and Brøns, Charlotte and Fonvig, Cilius Esmann and Holm, Jens-Christian and Nielsen, Trine and Pedersen, Julie Steen and Thiele, Maja Sofie and Trebicka, Jonel and Org, Elin and Krag, Aleksander and Hansen, Torben and Kuhn, Michael and Bork, Peer and Consortia, MicrobLiver and the GALAXY},journal={bioRxiv},year={2024},}
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
@article{AllertFerretti2024,title={Assembly, stability, and dynamics of the infant gut microbiome are linked to bacterial strains and functions in mother’s milk},author={Allert*, Mattea and Ferretti*, Pamela and Johnson, Kelsey and Heisel, Timothy and Gonia, Sara and Knights, Dan and Fields, David and Albert, Frank and Demerath, Ellen and Gale, Cheryl and Blekhman, Ran},journal={bioRxiv},year={2024},}
2023
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
@article{schmidt2023,title={SPIRE: a Searchable, Planetary-scale mIcrobiome REsource},author={Schmidt*, Thomas SB and Fullam*, Anthony and Ferretti, Pamela and Orakov, Askarbek and Maistrenko, Oleksandr and Ruscheweyh, Hans-Joachim and Letunic, Ivica and Duan, Yiqian and Van Rossum, Thea and Sunagawa, Shinichi and Mende, Daniel and Finn, Robert and Kuhn, Michael and Coelho, Luis Pedro and Bork, Peer},journal={Nucleic Acids Research},year={2023},publisher={Oxford University Press},}
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
@article{ferretti2023,title={C. difficile may be overdiagnosed in adults and is a prevalent commensal in infants},author={Ferretti, Pamela and Wirbel*, Jakob and Maistrenko*, Oleksandr M and Rossum*, Thea Van and Alves, Renato and Fullam, Anthony and Akanni, Wasiu and Schudoma, Christian and Schwarz, Anna and Thielemann, Roman and Thomas, Leonie and Kandels, Stefanie and Hercog, Rajna and Telzerow, Anja and Letunic, Ivica and Kuhn, Michael and Zeller, Georg and Schmidt, Thomas SB and Bork, Peer},journal={eLife},year={2023},}
2022
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
@article{klopp2022,title={Meconium microbiome of very preterm infants across Germany},author={Klopp, Jonas and Ferretti, Pamela and Meyer, Claudius U and Hilbert, Katja and Haiß, Annette and Marißen, Janina and Henneke, Philipp and Hudalla, Hannes and Pirr, Sabine and Viemann, Dorothee and Zemlin, Michael and Forslund, Sofia Kirke and Härtel, Christoph and Bork, Peer and Gehring, Stephan and Rossum, Thea Van and Consortium, PRIMAL},journal={MSphere},volume={7},number={1},pages={e00808-21},year={2022},publisher={American Society for Microbiology},}
Towards the biogeography of prokaryotic genes
Luis Pedro Coelho, Renato Alves, Álvaro Rodríguez Del Río, Pernille Neve Myers, Carlos P Cantalapiedra, Joaquín Giner-Lamia, Thomas Sebastian Schmidt, Daniel R Mende, Askarbek Orakov, Ivica Letunic, Falk Hildebrand, Thea Van Rossum, Sofia K Forslund, Supriya Khedkar, Oleksandr M Maistrenko, Shaojun Pan, Longhao Jia, Pamela Ferretti, Shinichi Sunagawa, Xing-Ming Zhao, Henrik Bjørn Nielsen, Jaime Huerta-Cepas, and Peer Bork
@article{coelho2022,title={Towards the biogeography of prokaryotic genes},author={Coelho, Luis Pedro and Alves, Renato and Río, Álvaro Rodríguez Del and Myers, Pernille Neve and Cantalapiedra, Carlos P and Giner-Lamia, Joaquín and Schmidt, Thomas Sebastian and Mende, Daniel R and Orakov, Askarbek and Letunic, Ivica and Hildebrand, Falk and Rossum, Thea Van and Forslund, Sofia K and Khedkar, Supriya and Maistrenko, Oleksandr M and Pan, Shaojun and Jia, Longhao and Ferretti, Pamela and Sunagawa, Shinichi and Zhao, Xing-Ming and Nielsen, Henrik Bjørn and Huerta-Cepas, Jaime and Bork, Peer},journal={Nature},volume={601},number={7892},pages={252--256},year={2022},publisher={Nature Publishing Group UK},}
2021
Characterization of 17 strains belonging to the Mycobacterium simiae complex and description of Mycobacterium paraense sp. nov.
Ana R Fusco Costa, Tarcisio Fedrizzi, Maria L Lopes, Monica Pecorari, Wana L Oliveira Costa, Elisabetta Giacobazzi, Jeann R Costa Bahia, Veronica De Sanctis, Karla V Batista Lima, Roberto Bertorelli, Antonella Grottola, Anna Fabio, Alessandro Mariottini, Pamela Ferretti, and others
International journal of systematic and evolutionary microbiology, 2021
@article{Costa2021,title={Characterization of 17 strains belonging to the Mycobacterium simiae complex and description of Mycobacterium paraense sp. nov.},author={da Costa, Ana R Fusco and Fedrizzi, Tarcisio and Lopes, Maria L and Pecorari, Monica and da Costa, Wana L Oliveira and Giacobazzi, Elisabetta and da Costa Bahia, Jeann R and Sanctis, Veronica De and Lima, Karla V Batista and Bertorelli, Roberto and Grottola, Antonella and Fabio, Anna and Mariottini, Alessandro and Ferretti, Pamela and others},journal={International journal of systematic and evolutionary microbiology},volume={65},number={2},pages={656--662},year={2021},publisher={Microbiology Society},}
Metagenomic assessment of the global diversity and distribution of bacteria and fungi
Mohammad Bahram, Tarquin Netherway, Clémence Frioux, Pamela Ferretti, Luis Pedro Coelho, Stefan Geisen, Peer Bork, and Falk Hildebrand
@article{bahram2021,title={Metagenomic assessment of the global diversity and distribution of bacteria and fungi},author={Bahram, Mohammad and Netherway, Tarquin and Frioux, Clémence and Ferretti, Pamela and Coelho, Luis Pedro and Geisen, Stefan and Bork, Peer and Hildebrand, Falk},journal={Environmental Microbiology},volume={23},number={1},pages={316--326},year={2021},publisher={John Wiley & Sons, Inc.},}
Experimental metagenomics and ribosomal profiling of the human skin microbiome
Falk Hildebrand, Toni I Gossmann, Clemence Frioux, Ezgi Özkurt, Pernille Neve Myers, Pamela Ferretti, Michael Kuhn, Mohammad Bahram, Henrik Bjørn Nielsen, and Peer Bork
@article{ferretti2018,title={Experimental metagenomics and ribosomal profiling of the human skin microbiome},author={Hildebrand, Falk and Gossmann, Toni I and Frioux, Clemence and Özkurt, Ezgi and Myers, Pernille Neve and Ferretti, Pamela and Kuhn, Michael and Bahram, Mohammad and Nielsen, Henrik Bjørn and Bork, Peer},journal={Experimental dermatology},volume={26},number={3},pages={211--219},year={2021},}
Dispersal strategies shape persistence and evolution of human gut bacteria
Falk Hildebrand, Toni I Gossmann, Clemence Frioux, Ezgi Özkurt, Pernille Neve Myers, Pamela Ferretti, Michael Kuhn, Mohammad Bahram, Henrik Bjørn Nielsen, and Peer Bork
@article{hildebrand2021,title={Dispersal strategies shape persistence and evolution of human gut bacteria},author={Hildebrand, Falk and Gossmann, Toni I and Frioux, Clemence and Özkurt, Ezgi and Myers, Pernille Neve and Ferretti, Pamela and Kuhn, Michael and Bahram, Mohammad and Nielsen, Henrik Bjørn and Bork, Peer},journal={Cell Host & Microbe},volume={29},number={7},pages={1167--1176},year={2021},publisher={Elsevier},}
2020
Diversity within species: interpreting strains in microbiomes
Thea Van Rossum*, Pamela Ferretti*, M. Oleksandr Maistrenko*, and Peer Bork
@article{vanrossum2020,title={Diversity within species: interpreting strains in microbiomes},author={Rossum*, Thea Van and Ferretti*, Pamela and Maistrenko*, M. Oleksandr and Bork, Peer},journal={Nature Reviews Microbiology},volume={18},number={1},pages={491--506},year={2020},publisher={Elsevier},}
2018
The short-term impact of probiotic consumption on the oral cavity microbiome
Erik Dassi*, Pamela Ferretti*, Giuseppina Covello, Roberto Bertorelli, Michela A Denti, Veronica De Sanctis, Adrian Tett, and Nicola Segata
@article{dassi2028,title={The short-term impact of probiotic consumption on the oral cavity microbiome},author={Dassi*, Erik and Ferretti*, Pamela and Covello, Giuseppina and Bertorelli, Roberto and Denti, Michela A and Sanctis, Veronica De and Tett, Adrian and Segata, Nicola},volume={8},number={1},pages={10476},year={2018},publisher={Nature Publishing Group UK},}
Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life
Moran Yassour, Eeva Jason, Larson J. Hogstrom, Timothy D. Arthur, Surya Tripathi, Heli Siljander, Jenni Selvenius, Sami Oikarinen, Heikki Hyöty, Suvi M. Virtanen, Jorma Ilonen, Pamela Ferretti, Edoardo Pasolli, Adrian Tett, Francesco Asnicar, Nicola Segata, Hera Vlamakis, Eric S. Lander, Curtis Huttenhower, Mikael Knip, and Ramnik J. Xavier
@article{YASSOUR2018146,title={Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life},journal={Cell Host & Microbe},volume={24},number={1},pages={146-154.e4},year={2018},publisher={Elsevier},issn={1931-3128},doi={https://doi.org/10.1016/j.chom.2018.06.007},url={https://www.sciencedirect.com/science/article/pii/S1931312818303196},author={Yassour, Moran and Jason, Eeva and Hogstrom, Larson J. and Arthur, Timothy D. and Tripathi, Surya and Siljander, Heli and Selvenius, Jenni and Oikarinen, Sami and Hyöty, Heikki and Virtanen, Suvi M. and Ilonen, Jorma and Ferretti, Pamela and Pasolli, Edoardo and Tett, Adrian and Asnicar, Francesco and Segata, Nicola and Vlamakis, Hera and Lander, Eric S. and Huttenhower, Curtis and Knip, Mikael and Xavier, Ramnik J.},}
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
@article{ferretti2018mother,title={Mother-to-infant microbial transmission from different body sites shapes the developing infant gut microbiome},author={Ferretti, Pamela and Pasolli, Edoardo and Tett, Adrian and Asnicar, Francesco and Gorfer, Valentina and Fedi, Sabina and Armanini, Federica and Truong, Duy Tin and Manara, Serena and Zolfo, Moreno and others},journal={Cell host \& microbe},volume={24},number={1},pages={133--145},year={2018},publisher={Elsevier},}
2017
Maternal inheritance of bifidobacterial communities and bifidophages in infants through vertical transmission
@article{duranti2017,title={Maternal inheritance of bifidobacterial communities and bifidophages in infants through vertical transmission},author={Duranti, Sabrina and Lugli, Gabriele Andrea and Mancabelli, Leonardo and Armanini, Federica and Turroni, Francesca and James, Kieran and Ferretti, Pamela and Gorfer, Valentina and Ferrario, Chiara and others},journal={Microbiome},volume={5},number={1},pages={1--3},year={2017},publisher={BioMed Central},}
Studying vertical microbiome transmission from mothers to infants by strain-level metagenomic profiling
Francesco Asnicar, Serena Manara, Moreno Zolfo, Duy Tin Truong, Matthias Scholz, Federica Armanini, Pamela Ferretti, Valentina Gorfer, Anna Pedrotti, Adrian Tett, and Nicola Segata
@article{ASNICAR2017,title={Studying vertical microbiome transmission from mothers to infants by strain-level metagenomic profiling},journal={mSystems},volume={2},number={1},year={2017},pages={e00164--16},publisher={ASM Journals},doi={https://doi.org/10.1128/mSystems.00164-16},url={https://journals.asm.org/doi/full/10.1128/msystems.00164-16},author={Asnicar, Francesco and Manara, Serena and Zolfo, Moreno and Truong, Duy Tin and Scholz, Matthias and Armanini, Federica and Ferretti, Pamela and Gorfer, Valentina and Pedrotti, Anna and Tett, Adrian and Segata, Nicola},}