Exploring the Microbiome of Korean Industrial Kimchi Fermentation Products

Despite existing over millenniums, Kimchi, a historic side dish of Korean culture, has a cultivation process that remains poorly defined and difficult to control along industrial production lines. Traditionally, Kimchi is made through the process of fermentation, a chemical mechanism in which microorganisms convert sugars to alcohol or an acid. The variation in taste existing across different batches of identically prepared kimchi products supports the idea that the constituents of the kimchi microbiome are generally unknown. The primary objective of this research study is to identify novel phages from fermented microbiomes, specifically within the kimchi microbiome. Furthermore, novel phages could have the capacity to serve as biocontrol agents. The secondary objective of this research study is to identify all microorganisms on a species level to allow the public to fully appreciate the diversity of the kimchi microbiome. Next-generation sequencing (NGS), a tool used to sequence the genetic material of organisms, will be used to identify the kimchi microbiome and continue downstream bioinformatics. Our preliminary analysis on an NGS data set from Korean industrial kimchi products with NCBI accession number of SRX2725663 will be used extensively throughout our research. We utilized six software packages with customized settings in order to analyze the datasets: Kraken2, Trimmonmatic, Velvet, Edena, BLAST, and Seaview. Kraken2 was used to distinguish novel sequences from previously characterized phages and bacterial hosts. After the identification of potential uncharacterized phages, researchers on the project may seek to develop the complete genomes of such phages. Additionally, researchers could use the generated databases from their bioinformatics pipeline to serve as a universally adopted protocol in the detection of novel phages. The utilization of this detection apparatus could reduce the pathogenic bacteria in food microbiomes