Discovering unique microbes made easy using the DOE Systems Biological Knowledge Base (KBase)


microbes It is the basis of life on earth. These microorganisms play a major role in everything from converting sunlight to molecules essential for life. It helps produce a lot of oxygen in our atmosphere. They even rotate feeders between air and Soil. Scientists are constantly finding interactions between Microbes, plants, animals, and other macroscopic life forms. As genomic sequencing advances, researchers can investigate not only isolated microbes, but entire communities of microorganisms — known as the microbiome — based on DNA found in the environment. the genome extracted from these communities (metagenomic sequencing) can identify organisms that carry out biogeochemical processes, contribute to health or disease in the human gastrointestinal microbiome, or interact with plant roots in Roots. the Department of Energy systems biology knowledge base (KBase) It recently released a feature set and protocol for performing cutting-edge microbiome analysis that could accelerate research into microbial ecology.

the influence

Widespread adoption of DNA sequencing in microbiology It produced huge amounts of genomic data. Researchers need computational tools to recover high-quality genomes from environmental samples to understand which organisms live in the environment and how they might interact. The combination of usability, data, and bioinformatics tools in a public online resource makes KBase a uniquely powerful web platform to perform this task. These new features in KBase will allow biologists to obtain genomes from microbiome sequences using easy-to-use software powered by DOE computational resources. This will reduce the time needed to process sequencing data and characterize the genome. Scientists can use KBase for analysis collaboratively Genomics data and build research communities to solve common problems in microbial ecology.


Obtaining the genomes of uncultured microbes directly from the environment using DNA sequencing is a recent advance that allows scientists to discover and characterize new organisms. Sequencing the DNA of all the microbes in a given environment results in a ‘metagenome’. Performing genetic analysis of metagenomes emerged as a method for exploring microbial traits and behaviors and community interactions in an ecological context. Methods for obtaining assembled metagenome genomes (MAGs) have varying degrees of success, depending on the techniques used. An increasing number of researchers are generating microbiome sequences, but many do not have ready access to the computational expertise, tools, and resources needed to extract, evaluate, and analyze their own genomes.

The KBase team has added and updated several metagenomic analysis tools, data types, and implementation capabilities to provide researchers with tools that accelerate discovery of microbial genomes and reveal the genetic potential of microbial communities. A recent paper in Nature Protocols presents a series of analysis steps, using KBase applications and data products to extract high-quality MAGs from metagenomes. These capabilities, including computing, data warehousing, data sharing, and analytics, are provided free to the public via the KBase web platform. This protocol allows scientists to generate putative genomes from organisms that only exist in the environment and analyze them using tools to understand who they are, what they do, with whom they interact, and their role in the ecosystem.


KBase is funded by the Genomic Sciences Program in the Department of Energy, Office of Science, Office of Biological and Environmental Research.

Journal link: Nature Protocols

Leave a Comment