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Methods to Assess Microbial Communities

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Related Experiment Video

Updated: May 21, 2026

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples

Published on: December 22, 2014

Computational Microbial and Viral Ecology Analysis.

James C Kosmopoulos^1,2, Karthik Anantharaman^3,4

¹Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.

Methods in Molecular Biology (Clifton, N.J.)

|May 19, 2026

Summary

This summary is machine-generated.

This guide presents a comprehensive workflow for jointly analyzing microbial communities and their viruses. It details bioinformatics methods for integrated metagenome and virome analysis, crucial for understanding microbial ecosystems.

Keywords:

Bacteriophage Host-virus interactions Metagenomics Microbial ecology Viral ecology Viromics

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Isolation and Genome Analysis of Single Virions using 'Single Virus Genomics'

Isolation and Genome Analysis of Single Virions using 'Single Virus Genomics'

Published on: May 26, 2013

Area of Science:

Microbiology
Bioinformatics
Computational Biology

Background:

Microbial communities are complex ecosystems with significant interactions between bacteria, archaea, and viruses.
Understanding these interactions is vital for a complete picture of environmental microbiomes.
Existing protocols for simultaneous analysis of prokaryotes and viruses are limited.

Purpose of the Study:

To provide a beginner-friendly, comprehensive protocol for the joint analysis of metagenome and virome data.
To guide researchers with limited bioinformatics experience in multiscale microbiome analysis.
To ensure adherence to best practices in microbial and metagenomic data analysis.

Main Methods:

Development of an expansive bioinformatics workflow for integrated metagenome and virome analysis.
Detailed steps covering study design, sequence processing, assembly, and quality control.
Includes virus identification, genome binning, taxonomic characterization, and host-virus prediction.

Main Results:

The workflow enables simultaneous analysis of microbial communities and associated viruses.
Provides bioinformatic scripts for reuse in computational methods.
Offers guidance on subsequent data processing and analysis approaches.

Conclusions:

Integrated analysis of metagenomes and viromes is essential for a holistic understanding of microbial ecosystems.
This protocol simplifies complex bioinformatics for researchers new to the field.
Facilitates advanced microbiome research through accessible, reusable computational tools.