KBase has a multitude of apps designed to analyze microbial communities and metagenomic reads data. They provide a way to understand the functional interactions between species in microbial communities. Annotated genomes extracted from metagenomic samples can be used for metabolic modeling, comparative phylogenomics, functional profiling, and more.
Metagenomic Sequence Analysis & Assembly
The interactive Genome Extraction from Shotgun Metagenome Sequence Data tutorial is a good way to understand an important metagenomic pipeline. The workflow is described in the image below.