A practical introduction to holo-omics

• Published in: Cell reports methods 2024-07, Vol.4 (7), p.100820, Article 100820
• Main Authors: Odriozola, Iñaki, Rasmussen, Jacob A., Gilbert, M. Thomas P., Limborg, Morten T., Alberdi, Antton
• Format: Article
• Language: English
• Subjects: Animals; Computational Biology - methods; CP: Genetics; CP: Microbiology; Genomics; Host Microbial Interactions - genetics; Humans; Metabolomics; Microbiota; Proteomics - methods; Review
• ISSN: 2667-2375; 2667-2375
• DOI: 10.1016/j.crmeth.2024.100820

Holo-omics refers to the joint study of non-targeted molecular data layers from host-microbiota systems or holobionts, which is increasingly employed to disentangle the complex interactions between the elements that compose them. We navigate through the generation, analysis, and integration of omics data, focusing on the commonalities and main differences to generate and analyze the various types of omics, with a special focus on optimizing data generation and integration. We advocate for careful generation and distillation of data, followed by independent exploration and analyses of the single omic layers to obtain a better understanding of the study system, before the integration of multiple omic layers in a final model is attempted. We highlight critical decision points to achieve this aim and flag the main challenges to address complex biological questions regarding the integrative study of host-microbiota relationships. The joint molecular study of animal and plant species along with their associated microorganisms is challenged by its complexity. Odriozola et al. review the generation, analysis, and integration of such data and highlight critical decision points aiming to improve study designs and analytical pipelines for better solving the puzzle of host-microbiota relationships.