Part 1: CLC Microbial Genomics Module


Jonathan Jacobs

Part 1: CLC Microbial Genomics Module

Functional metagenomics analysis of environmental microbiomes: A new white paper for the Microbial Genomics Module of CLC Genomics Workbench

Microbiome research presents us with an opportunity to study all microorganisms on Earth. Nonetheless, many are difficult to isolate in the lab and remain uncultured using traditional microbiology methods, despite more than 100 years of research into developing new cultivation methods. Unraveling the currently undiscovered biodiversity of microbiomes remains a major challenge in microbiology, and it is estimated that more that 99% of all microbes remains uncharacterized by traditional culture methods (1). Just 20 years ago, in 1998, Handelsman first proposed to analyze a soil microbial community without prior cultivation (2). The use of culture-independent metagenomics approaches grew rapidly once the advantages became clear, with just one publication listed in PubMed in 1998 to now more than 11,000 publications.

Metagenomic sequencing is a powerful approach to investigate the microbial diversity of complex samples, with taxonomic classification of organisms sometime reaching strain level precision. Shotgun metagenomics can not only reveal specific organisms in a sample, but is also a powerful approach to characterize the functional genomic profile encoded within microbiomes, and potentially to discover genes with new functions. Although the specific sample preparation, library preparation, and sequencing platform used are all important factors that influence the quality of your results, ultimately the downstream bioinformatics pipelines and reference databases used become the analysis bottleneck. With this last point in mind, we have released a new white paper describing how to carry out functional genomics characterization of unbiased shotgun metagenomics data using CLC Genomics Workbench and the add-on CLC Microbial Genomics Module.

To demonstrate the broad capabilities of our software, we re-analyzed previously published data from Mukan Ji and co-workers (3). Ji et al investigated the surprisingly diverse microbial soil community of a polar desert in Antarctica and sought to understand how these microbes survive in such a harsh and nutrient deficient habitat.

For an in-depth discussion of the study and their exciting findings, we recommend listening to the podcast with microbiology experts Vincent Racaniello, Michael Schmidt, Elio Schaechter, and Michelle Swanson on This Week in Microbiology, TWiM. The paper was discussed in Episode 169 – Breatharian Bacteria.

Read our white paper on functional metagenomics with CLC Genomics Workbench and the Microbial Genomics Module and learn how to reveal the functional potential of microbiomes sequenced using shotgun metagenomics methods.


  1. Lloyd K.G., et al. (2018). Phylogenetically Novel Uncultured Microbial Cells Dominate Earth Microbiomes. mSystems 3(5):e00055-18.
  2. Handelsman J. et al. (1998). Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol. 5(10):R245–9.
  3. Ji M., et al. (2017) Atmospheric trace gases support primary production in Antarctic desert surface soil. Nature 552(7685):400–3.