MetaFunPrimer

Amplifying a specific group of microbial functional genes from a complex soil sample is like catching a certain species of fish from an ocean. Imagine there is a special kind of bait that only attracts the fish species of interest, we hope to design some specific primers that only bind to and amplify the target functional gene group of interest.

The underground world harbors an important community: microbiomes. The soil microbial communities play important roles in ecosystem processes, such as nitrogen cycling. Microbiome genes belonging to the same functional group may include numerous and variable gene sequences, making characterizing and quantifying difficult. Therefore, high-throughput design tools are needed to simultaneously create primers for improved quantification of target genes. We developed MetaFunPrimer, a bioinformatic pipeline, to design primers for numerous genes of interest. This tool also enables gene target prioritization based on ranking the presence of genes in user-defined references, such as environment-specific metagenomes.

This new tool gives microbial ecologists a new approach to assess functional gene abundance and related microbial community dynamics quickly and affordable. This work has been published on mSystems. Check out the paper and its github page for more details.