User guide(Database usage instructions)

Microbial Genome database provides publicly available genomic data searching, downloading and sharing service, integrates genomic data analysis tools, and furthermore achieves genomic data online dynamic visual display.


Microbial genome database need to register as a user to obtain a login and password. Logins/passwords allow users to download microbial genome and metagenomic datasets and employ analysis tools for analyzing and visualizing these data. There are two types of user accounts available on our database. One is normal users who could download public data and manage their own genomic/ metagenomic datasets. The other is authenticated users (verified by the organization) who could apply for data storage and finally save their personal data in the database system. Normal users could apply for authenticated users at the personal information page.

Data distribution

The database integrates publicly available genome datasets involving Bacteria, Achaea, and Human, Environment-related , animal and plant

The microbial genome database containing registered users, 159754 data records,and 433128 related data files, in which includes 129311 genomes of bacterial strains, 29017 metagenomic data from human and environmental samples. The genome dataset contains 129311 strains public data, including 39208 bacteria strains, 694 archaea strains. The metagenomic dataset contains 29017 28816 samples, including 797 water samples, 2 air samples, 0 soil sample, 17970 human samples, 7 animal samples, 0 plant sample, and 10108 samples from others.

Data submission

If you already have downloaded the database client, submit your data according to the following process; If not, please download the client at first( data download/upload client),and then submit and download data via the client. )

Single data submission

Click the Add data option in the client pages, fill in the content according to the options given. Fields marked with "*" are required)

  • The acceptable format of raw data is fastq;
  • The format of QC data is fastq;
  • The format of assemble data is fastq;
  • The format of annotation data is txt;
  • The format of gene prediction data is file with suffix of cds、gff、pep, respectively
  • The diversity analys is data Upload in a compressed format.

Batch data import

download the data submission template in the web page(batch data submission template ), import the metadata into the batch submission template and save in Excel format. Click the button of batch data import in the web page, and then in the file dialog, navigate to your Excel file and click OK.

After importing the metadata sheet, select the datasets to be submitted, click “submission” option to submit data to personal database.

Application for storage(only for authenticated users)

Authenticated user could enter the personal data management interface in the web page, click on the storage application button, fill in the relevant information, and then import data to the database for review. Data audit will be conducted within 1-3 days after the application and the result of the audit will be communicated to the user by e-mail, and the status of the application could be checked on the page any instant.

Data download

Currently, the database only supports download via client(data download/upload client)to maximize the download speed. After Downloading and installing the client successfully, users could log in to download the corresponding data files using the ID number obtained from web pages search function.