  The explosion in known microbial diversity in the last two decades has made
it abundantly clear that microbes in the environment do not exist in isolation;
they are members of communities. Accordingly, omics approaches such as
metagenomics have revealed that interactions between diverse groups of
community members such as archaea, bacteria, and viruses (bacteriophage) are
common and have significant impacts on entire microbiomes. Thus, to have a
well-developed understanding of microbes as they naturally exist in the
environment, biological entities of all kinds must be studied together. While
numerous protocols for metagenome analysis exist, comprehensive published
protocols for the simultaneous analysis of viruses and prokaryotes together are
scarce. Further, as bioinformatic methods for microbiology rapidly advance,
existing metagenomic tools and pipelines require frequent reevaluation. This
ensures the adherence of best practices for microbiome and metagenomic data
analysis. Here, we offer an expansive approach for the joint analysis of bulk
sequence data from a mixed microbial community (metagenomes) and viral-sized
fraction communities (viromes). This chapter serves as a beginner's-level guide
for researchers with limited bioinformatics expertise who wish to engage in
multi-scale metagenome and virome analyses. We cover steps from initial study
design to sequence read processing, metagenome assembly, quality control, virus
identification, microbial and viral genome binning, taxonomic characterization,
species-level clustering, and host-virus predictions. We also provide the
bioinformatic scripts used in our workflow for reuse in one's own computational
methods. Lastly, we discuss additional approaches a researcher can take after
processing data with this workflow.
