Holo-Omics: Integrated Host-Microbiota Multi-omics for Basic and Applied Biological Research
Lasse Nyholm,
Adam Koziol,
Sofia Marcos,
Amanda Bolt Botnen,
Ostaizka Aizpurua,
Shyam Gopalakrishnan,
Morten T. Limborg,
M.Thomas P. Gilbert,
Antton Alberdi
Affiliations
Lasse Nyholm
Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen 1353, Denmark; Corresponding author
Adam Koziol
Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen 1353, Denmark
Sofia Marcos
Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa 48940, Spain
Amanda Bolt Botnen
Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen 1353, Denmark
Ostaizka Aizpurua
Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen 1353, Denmark
Shyam Gopalakrishnan
Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen 1353, Denmark; Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kongens Lyngby 2800, Denmark
Morten T. Limborg
Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen 1353, Denmark
M.Thomas P. Gilbert
Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen 1353, Denmark; Norwegian University of Science and Technology, University Museum, Trondheim 7491, Norway
Antton Alberdi
Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen 1353, Denmark
Summary: From ontogenesis to homeostasis, the phenotypes of complex organisms are shaped by the bidirectional interactions between the host organisms and their associated microbiota. Current technology can reveal many such interactions by combining multi-omic data from both hosts and microbes. However, exploring the full extent of these interactions requires careful consideration of study design for the efficient generation and optimal integration of data derived from (meta)genomics, (meta)transcriptomics, (meta)proteomics, and (meta)metabolomics. In this perspective, we introduce the holo-omic approach that incorporates multi-omic data from both host and microbiota domains to untangle the interplay between the two. We revisit the recent literature on biomolecular host-microbe interactions and discuss the implementation and current limitations of the holo-omic approach. We anticipate that the application of this approach can contribute to opening new research avenues and discoveries in biomedicine, biotechnology, agricultural and aquacultural sciences, nature conservation, as well as basic ecological and evolutionary research.
