The Alpine ibex (Capra ibex) gut microbiome, seasonal dynamics, and potential application in lignocellulose bioconversion
Enrico Nanetti,
Daniel Scicchitano,
Giorgia Palladino,
Nicolò Interino,
Luca Corlatti,
Luca Pedrotti,
Federica Zanetti,
Elena Pagani,
Erika Esposito,
Alice Brambilla,
Stefano Grignolio,
Ilaria Marotti,
Silvia Turroni,
Jessica Fiori,
Simone Rampelli,
Marco Candela
Affiliations
Enrico Nanetti
Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
Daniel Scicchitano
Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy; Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, 61032 Fano, Italy
Giorgia Palladino
Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy; Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, 61032 Fano, Italy
Nicolò Interino
Department of Chemistry “G. Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy
Luca Corlatti
Stelvio National Park, 23032 Bormio, Italy; University of Freiburg, 79098 Freiburg, Germany
Luca Pedrotti
Stelvio National Park, 23032 Bormio, Italy
Federica Zanetti
Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 44, 40127 Bologna, Italy
Elena Pagani
Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 44, 40127 Bologna, Italy
Erika Esposito
Department of Chemistry “G. Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy
Alice Brambilla
Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich (CH), Switzerland; Centro Studi Fauna Alpina, Parco Nazionale Gran Paradiso, Loc. Degioz 11, 11010 Valsavarenche, Aosta, Italy
Stefano Grignolio
University of Ferrara, Department of Life Science and Biotechnology, via Borsari 46, I-44121 Ferrara, Italy
Ilaria Marotti
Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 44, 40127 Bologna, Italy
Silvia Turroni
Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
Jessica Fiori
Department of Chemistry “G. Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy
Simone Rampelli
Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy; Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, 61032 Fano, Italy
Marco Candela
Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy; Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, 61032 Fano, Italy; Corresponding author
Summary: Aiming to shed light on the biology of wild ruminants, we investigated the gut microbiome seasonal dynamics of the Alpine ibex (Capra ibex) from the Central Italian Alps. Feces were collected in spring, summer, and autumn during non-invasive sampling campaigns. Samples were analyzed by 16S rRNA amplicon sequencing, shotgun metagenomics, as well as targeted and untargeted metabolomics. Our findings revealed season-specific compositional and functional profiles of the ibex gut microbiome that may allow the host to adapt to seasonal changes in available forage, by fine-tuning the holobiont catabolic layout to fully exploit the available food. Besides confirming the importance of the host-associated microbiome in providing the phenotypic plasticity needed to buffer dietary changes, we obtained species-level genome bins and identified minimal gut microbiome community modules of 11–14 interacting strains as a possible microbiome-based solution for the bioconversion of lignocellulose to high-value compounds, such as volatile fatty acids.
