Evaluation of the impact of sequencing depth and choice of bioinformatics methods in the taxonomic and functional profiling of the honeybee (Apis mellifera) microbiome
Ortega Polo, R., Gregoris, A., Tran, L., Vishwakarma, S. & Guarna, M. M. Evaluation of the impact of sequencing depth and choice of bioinformatics methods in the taxonomic and functional profiling of the honeybee (Apis mellifera) microbiome. 28th Conference on Intelligent Systems for Molecular Biology. Virtual conference. July 13-16, 2020
Plain language summary
Pollination services provided by bees are essential for Canadian agriculture. The honeybee gut microbiome is a community of microorganisms that is linked to bee health and immunity. There are different approaches for obtaining information from those communities of microorganisms using DNA sequencing. For example, we can focus on a small target region of the 16S gene that can help us distinguish different taxa, or we can sequence everything in a sample using a method called shotgun metagenomic sequencing. In this work, our team analyzed microbial community profiles studied with both sequencing approaches, but we also compared the effect of sample type (using whole bees, whole abdomens, whole guts and hindguts) and of sequencing depth (how much information we get from the DNA sequences in the sample). The goal is to help inform bee microbiome researches of the effect of different sample types, amount of information and sequencing approach before planning large scale sequencing projects.
Honeybees make a crucial contribution to Agriculture through their pollination services. The diverse members of the honey bee gut microbiome have a symbiotic and/or pathogenic relationship with bees, and they directly impact bee health and immunity. Recent studies have highlighted the role of metagenomic sequencing in gaining a better understanding of both the microbiome composition and the functional profiles of the honeybee gut microbial communities. In this study, we evaluated the impact of sequencing depth on the taxonomic and functional profiling of the honeybee gut microbiome using metagenomic sequencing. Furthermore, we compared analytic methods to characterize de novo metagenomic assemblies, and we compared the resolution of shotgun metagenomic data and 16S rRNA microbial community profiling for the characterization of bacterial members within the honey bee microbiome. In this work we compared existing methods that use the Snakemake and Nextflow workflow management systems for reproducible, portable, and re-usable methods for profiling and de novo assemblies. We also developed an R-based reproducible pipeline that integrates DADA2 and phyloseq using the Drake workflow management system. The work presented here will help inform decisions on methodological approaches for large-scale bee microbiome studies tailored to specific research questions in bee health and nutrition.