MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice
Paolo Manghi,
Aitor Blanco-Míguez,
Serena Manara,
Amir NabiNejad,
Fabio Cumbo,
Francesco Beghini,
Federica Armanini,
Davide Golzato,
Kun D. Huang,
Andrew M. Thomas,
Gianmarco Piccinno,
Michal Punčochář,
Moreno Zolfo,
Till R. Lesker,
Marius Bredon,
Julien Planchais,
Jeremy Glodt,
Mireia Valles-Colomer,
Omry Koren,
Edoardo Pasolli,
Francesco Asnicar,
Till Strowig,
Harry Sokol,
Nicola Segata
Affiliations
Paolo Manghi
Department CIBIO, University of Trento, Trento, Italy
Aitor Blanco-Míguez
Department CIBIO, University of Trento, Trento, Italy
Serena Manara
Department CIBIO, University of Trento, Trento, Italy
Amir NabiNejad
Department CIBIO, University of Trento, Trento, Italy; IEO, European Institute of Oncology IRCCS, Milan, Italy
Fabio Cumbo
Department CIBIO, University of Trento, Trento, Italy
Francesco Beghini
Department CIBIO, University of Trento, Trento, Italy
Federica Armanini
Department CIBIO, University of Trento, Trento, Italy
Davide Golzato
Department CIBIO, University of Trento, Trento, Italy
Kun D. Huang
Department CIBIO, University of Trento, Trento, Italy
Andrew M. Thomas
Department CIBIO, University of Trento, Trento, Italy
Gianmarco Piccinno
Department CIBIO, University of Trento, Trento, Italy
Michal Punčochář
Department CIBIO, University of Trento, Trento, Italy
Moreno Zolfo
Department CIBIO, University of Trento, Trento, Italy
Till R. Lesker
Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
Marius Bredon
Gastroenterology Department, Sorbonne Université, INSERM, Centre de Recherche Saint Antoine, CRSA, AP-HP, Saint Antoine Hospital, 75012 Paris, France; Paris Centre for Microbiome Medicine (PaCeMM) FHU, Paris, France
Julien Planchais
Paris Centre for Microbiome Medicine (PaCeMM) FHU, Paris, France; INRAE, UMR1319 Micalis & AgroParisTech, Jouy en Josas, France
Jeremy Glodt
Paris Centre for Microbiome Medicine (PaCeMM) FHU, Paris, France; INRAE, UMR1319 Micalis & AgroParisTech, Jouy en Josas, France
Mireia Valles-Colomer
Department CIBIO, University of Trento, Trento, Italy
Omry Koren
Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
Edoardo Pasolli
Department of Agricultural Sciences, University of Naples, Naples, Italy
Francesco Asnicar
Department CIBIO, University of Trento, Trento, Italy
Till Strowig
Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany; Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
Harry Sokol
Gastroenterology Department, Sorbonne Université, INSERM, Centre de Recherche Saint Antoine, CRSA, AP-HP, Saint Antoine Hospital, 75012 Paris, France; Paris Centre for Microbiome Medicine (PaCeMM) FHU, Paris, France; INRAE, UMR1319 Micalis & AgroParisTech, Jouy en Josas, France
Nicola Segata
Department CIBIO, University of Trento, Trento, Italy; IEO, European Institute of Oncology IRCCS, Milan, Italy; Corresponding author
Summary: Mouse models are key tools for investigating host-microbiome interactions. However, shotgun metagenomics can only profile a limited fraction of the mouse gut microbiome. Here, we employ a metagenomic profiling method, MetaPhlAn 4, which exploits a large catalog of metagenome-assembled genomes (including 22,718 metagenome-assembled genomes from mice) to improve the profiling of the mouse gut microbiome. We combine 622 samples from eight public datasets and an additional cohort of 97 mouse microbiomes, and we assess the potential of MetaPhlAn 4 to better identify diet-related changes in the host microbiome using a meta-analysis approach. We find multiple, strong, and reproducible diet-related microbial biomarkers, largely increasing those identifiable by other available methods relying only on reference information. The strongest drivers of the diet-induced changes are uncharacterized and previously undetected taxa, confirming the importance of adopting metagenomic methods integrating metagenomic assemblies for comprehensive profiling.
