Exploring the Microbiome of Korean Industrial Kimchi Fermentation Products
Disciplines
Bioinformatics | Computational Biology | Food Microbiology | Genomics
Abstract (300 words maximum)
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 objective of this research study is to classify microbial species from Korean industrial kimchi fermentation products and potentially discover novel phages. Next-generation sequencing (NGS), a tool used to sequence the genetic material of organisms, will be used to probe the kimchi microbiome and continue downstream bioinformatics. Shotgun metagenomic sequencing, a technique of genome reassembly through regions of nucleotide overlap, will be used via a pipeline containing four software packages with customized settings in order to analyze the datasets: CutAdapt, Kraken2, Spades and BLAST. Our preliminary analysis on an NGS data set from Korean industrial kimchi products with NCBI accession number of SRX2725663 was used extensively throughout our research. 99.11% of the metagenome was identified, and .89% of unclassified reads remain. Of the reads identified, probiotics such as Weissella confusa and Bifidobacterium gallicum were present. Additionally, the presence of Escherichia coli and Enterococcus faecium are indicative of potential fecal contamination in the sample. Downstream analysis of unclassified reads will include BLAST searches. Furthermore, researchers on the project may seek to develop the complete genomes of phages as they have been known to have the capacity to serve as biocontrol agents.
Academic department under which the project should be listed
CSM - Molecular and Cellular Biology
Primary Investigator (PI) Name
Dr. Tsai-Tien Tseng
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 objective of this research study is to classify microbial species from Korean industrial kimchi fermentation products and potentially discover novel phages. Next-generation sequencing (NGS), a tool used to sequence the genetic material of organisms, will be used to probe the kimchi microbiome and continue downstream bioinformatics. Shotgun metagenomic sequencing, a technique of genome reassembly through regions of nucleotide overlap, will be used via a pipeline containing four software packages with customized settings in order to analyze the datasets: CutAdapt, Kraken2, Spades and BLAST. Our preliminary analysis on an NGS data set from Korean industrial kimchi products with NCBI accession number of SRX2725663 was used extensively throughout our research. 99.11% of the metagenome was identified, and .89% of unclassified reads remain. Of the reads identified, probiotics such as Weissella confusa and Bifidobacterium gallicum were present. Additionally, the presence of Escherichia coli and Enterococcus faecium are indicative of potential fecal contamination in the sample. Downstream analysis of unclassified reads will include BLAST searches. Furthermore, researchers on the project may seek to develop the complete genomes of phages as they have been known to have the capacity to serve as biocontrol agents.