Challenge: Company lacked the right bioinformatics tools and expertise required for large-scale metagenomic analysis
An agricultural company sought to manipulate methane production in cows by delving into the complex microbial ecosystem within the cow’s rumen. Instead of focusing on a single genome, the study required analyzing the entire community of microorganisms.
The company needed to confirm the presence of methanogens (microbes responsible for methane production). Then, monitor how gene expression in these organisms changed in response to various treatments.
The company lacked the specialized bioinformatics tools and expertise required to conduct large-scale metagenomic analysis and reliably quantify the key gene orthologs involved in methane production.
Action: Diamond Age partnered with the agricultural company to develop the necessary bioinformatics tools. This included:
- Custom Workflow Development: We designed and built a specialized workflow to process and analyze metagenomic sequencing data. By utilizing tools such as Megahit, we created a custom genome set tailored specifically to the methanogens present in the cow’s rumen.
- Data Alignment and Quantification: Our workflow accurately aligned sequencing data against the custom methanogen genome set, enabling precise quantification of gene orthologs involved in methane production. This approach allowed for reliable tracking of gene expression changes over time in response to different treatments.
- Knowledge Transfer and Collaboration: Initially engaged as external experts to kick-start the project, we developed the workflow and then transferred our knowledge to an in-house bioinformatician. This collaborative approach ensured that the client could continue refining and applying the analysis independently.
Result: A robust, scalable, and accurate workflow
Our collaborative bioinformatics consulting engagement delivered significant and lasting benefits. The client now has a robust, scalable workflow that accurately quantifies gene expression changes in methanogens. This allows for ongoing monitoring of the cow’s rumen microbiome and yields valuable insights into the effects of various treatments on methane production.
The advanced workflow not only establishes a strong foundation for future metagenomic studies but also enhances the client’s ability to refine strategies for controlling methane production. This ultimately positions them to implement environmentally beneficial solutions.
Lacking the bioinformatics analysis tools you need to achieve your goals? Please contact us at contact@diamondage.com or visit https://diamondage.com/contact/.