MetaMetaDB is a comprehensive and searchable meta-16S database.




Ching-Chia Yang
Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Japan.
chia AT


Creative Commons License


Why MetaMetaDB?

The habitats of a microbe can provide pertinent information for understanding the physiology, evolution, and interaction of the microbe within microbial communities. Therefore, identifying where a species exists is the first step in the study of microbiology. Generally, 16S rRNA sequences are used for the taxonomical assignment of microbes and thus are the basic information for identifying the microbes in an environment. However, current 16S rRNA databases lack information regarding environments and are biased to culturable microbes. Fortunately, metagenomic studies, which focus on the entire microbial community rather than one species, have produced millions of nucleotide sequences from the microbial communities of various environments. These sequences contain abundant 16S rRNA sequences of culturable and unculturable microbes from different environments. Therefore, these 16S rRNA sequences can be used as a reference source for microbial species from all over the world.

To search for possible habitats of microbes, we have collected 16S rRNA sequences generated by Roche 454 platforms to create MetaMetaDB. Comparing a particular 16S rRNA sequence(s) with the representative 16S rRNA sequences from different environments using BLAST, MetaMetaDB calculates the Microbial Habitability Index (MHI) in each environment to infer the possibility of finding that microbe(s) in each environment.

Q & A

=== Please note that the figures and statisticas beneath are generated by the dataset of version 1 (see the archive). ===

Q1. How to use MetaMetaDB? [Expand/Hide]

Q2. How does MetaMetaDB find the habitats of my microbes? [Expand/Hide]

Q3. What does the output mean? [Expand/Hide]

Q4. I have several 16S rRNA sequences and I want to treat them as one group. What should I do? [Expand/Hide]

Q5. In Download page, there are environments such as "marine", "soil", and "gut." What are these terms? [Expand/Hide]

Q6. How were the 16S rRNA sequences generated? [Expand/Hide]

Q7. I want to know the precise places where my microbes can be found. Why is that impossible? [Expand/Hide]