Metagenomic & Community Analysis

Running Metagenomic and community analysis in KBase

KBase has a multitude of tools 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.

Narrative Tutorials

• Genome Extraction from Shotgun Metagenome Sequence Data – this is a good example for understanding a metagenomic pipeline.

• Using Metagenomes to Discover Novel Microbial Linages in KBase – demonstrates the application of bioinformatic tools for metagenome assembly and genome binning. This Narrative highlights the effective use of employing multiple genome binners and a bin optimization approach.

• Metagenome-Assembled Genome Extraction from a Compost Microbiome Enrichment – demonstrates an in-depth example of metagenome-assembled genome extraction and analysis to obtain high-quality genomes.

  • Chivian et al. (2023) Metagenome-assembled genome extraction and analysis from microbiomes using KBase. Nature Protocols 18, 208-238. https://doi.org/10.1038/s41596-022-00747-x

  • Compare and contrast the enriched environment sample analysis to a Moab Desert Crust environmental sample.

• The PlantSEED Resource in KBase – shows the streamlined process of annotating plant genome sequences, automatically constructing metabolic models based on genome annotations, and using models to test annotations.

Microbiome Fractionation by Genome Extraction

Functional and Taxonomic Profiling of Metagenome-Assembled Genomes

Metagenome-assembled Genome Extraction and Analysis Tutorial Webinar