BiomeSeq: A Tool for the Characterization of Animal Microbiomes from Metagenomic Data

Abstract

The complete characterization of a microbiome is critical in elucidating the complex ecology of the microbial composition within healthy and diseased animals. Many microbiome studies characterize only the bacterial component, for which there are several well-developed sequencing methods, bioinformatics tools and databases available. The lack of comprehensive bioinformatics workflows and databases have limited efforts to characterize the other components existing in a microbiome. BiomeSeq is a tool for the analysis of the complete animal microbiome using metagenomic sequencing data. With its comprehensive workflow, customizable parameters and microbial databases, BiomeSeq can rapidly quantify the viral, fungal, bacteriophage and bacterial components of a sample and produce informative tables for analysis. BiomeSeq was employed in detecting and quantifying the respiratory microbiome of a commercial poultry broiler flock throughout its grow-out cycle from hatching to processing. It successfully processed 780 million reads, of which 5,163 aligned to avian DNA viral genomes, 71,936 aligned to avian RNA viral genomes, 469,937 aligned to bacterial genomes, 504,682 aligned to bacteriophage genomes and 1,964 aligned to fungal genomes. For each microbial species detected, BiomeSeq calculated the normalized abundance, percent relative abundance, and coverage as well as the diversity for each sample. BiomeSeq provides for the detection and quantification of the microbiome from next-generation metagenomic sequencing data. This tool is implemented into a user-friendly container that requires one command and generates a table consisting of taxonomical information for each microbe detected as well as normalized abundance, percent relative abundance, coverage and diversity calculations.