Kimchi is a traditional side dish made from salted and fermented vegetables. When the fermentation is right, the pH of the cabbage kimchi reaches ~4.2. When it is fully matured, the microbial community comprises of lactic acid bacteria. Because no defined starter cultures are used in even commercial production, the diversity of these lactic acid bacteria is not certain. In this tutorial, we will explore and compare the microbial community of commercially produced kimchi.
The mature cabbage kimchi products were purchased and sequenced by Roche 454 sequencing. See here for the details of the study.
1. Login to www.ezbiocloud.net (It’s free to create an account).
2. Open [Apps] at the top-right corner of the screen.
3. Click [MTP] to start Microbiome Taxonomic Profile service.
4. Now, we need to check out data from the public microbiome database of EzBioCloud. Click [+Public database] at the left panel. This will lead you to <EzBioCloud Microbiome Database>.
5. (a) Find the project called “Bacterial community of mature cabbage Kimchi” and (b) check all MTPs out.
6. Go back to your MTP main page. You should be able to see all kimchi MTPs (samples) in your account.
7. (a) Select all kimchi MTPs and (b) create a set for them. Now, all kimchi MTPs are grouped in a set, named “Kimchi”.
8. Select the set to compare kimchi communities by different manufacturers by clicking [Set] at the right side of the screen. [Set] menu will be pulled out.
9. Open the “Kimchi” set and go to [Composition].
10. Because sequencing reads included in each MTP are different, comparison of various statistical values may not be viable. You can normalize with the same sequencing reads in EzBioCloud. Click [Normalize] on the left panel and set “Read count” to 1,000 reads.
11. Compare compositions at the phylum to species level.
12. Compare ACE species richness (=number of species) and Shanon diversity index in [Alpha Diversity]
13. See how the kimchi communities are related by using analytics provided in the [Beta Diversity].
Last edited Oct. 25, 2017/ JC