About the COLOSS Wiki Initiative
In the past decades, COLOSS members have joined forces multiple times to develop and condense standard methods related to honey bees, their pests, pathogens, and hive products. This led to the open access of four BEEBOOK volumes that have been enthusiastically welcomed by honey bee researchers worldwide. Among the chapters, the “Standard methods for molecular research in Apis mellifera ” written by Evans and collaborators in 2013 has been a cornerstone for the standardization of honey bee molecular studies. However, since sequencing technologies and analyzing algorithms have made tremendous progress, many described methods needed a refreshing update. In parallel, other Apis species genomes have been sequenced, thus opening new research avenues in a comparative framework.
Advancing Multi-Omics Research Reproducibility
Our team has spent the last years developing and summarizing new protocols related to the recent multi-omics field advances in a new chapter entitled “Standard methods and good practices in Apis honey bee ‘omics research.” At the same time, next-generation sequencing and bioinformatics will continue to improve and change, mirroring how the multi-omics field is rapidly evolving. As a result, we concluded that a classical chapter would become outdated unless we adopted a modern communication approach.
Online shared resources such as databases, codes, Wikis, and tutorials are great ways to provide protocols in a dynamic and collaborative framework. We propose here a set of standard protocols related to applications of genomics, transcriptomics, proteomics, epigenomics, metabolomics, metagenomics, and microbiome analyses in Apis honey bees. One advantage of this platform will be version control of methods, which can be corrected and improved by the developing team at the suggestion of COLOSS members or experts. This would allow readers to track major changes related to the progress of wet lab techniques or computing pipelines.
While initially, omics data are often created for highly specialized scope and research questions, we noted that Apis honey bee research slowly moves toward multi-omics integration. This transition will push the boundaries of our understanding regarding honey bee biology and evolution. However, this would require the establishment of resources to aid communication, information sharing about tools and techniques, and data interpretation between different teams of honey bee experts. We hope that this chapter will lay some foundations by reviewing jargon and tools specific to each omic field and support the communication of innovative studies taking advantage of large and complex datasets.
The methods and tutorials described here are still part of the chapter “Standard Methods and Good Practices in Apis Honey Bee ‘Omics Research” in BEEBOOK Volume IV. If these resources are useful for you, please cite our work: “Techer, M.A., Chakrabarti, P., Caesar, L., Eynard, S.E., Farrell, M.C., Foster, L.J., Gorrochategui-Ortega, J., Henriques, D., Li-Byarlay, H., Morre, J.T., Newton, I.L.G., Parejo, M., Pinto, M.A., Vignal, A., Zarraonaindia, I., McAfee, A. (2025) Standard methods and good practices in Apis honey bee ‘omics research. In P. Chantawannakul, J.D. Evans, P. Neumann, N. L. Carreck, J. D. Ellis & V. Dietemann (Eds.), The COLOSS BEEBOOK, Volume IV: Standard methods for Apis cerana research and Apis ‘omics. Journal of Apicultural Research, 64(2)."