Details

Title: RIM-DB: a taxonomic framework for community structure analysis of methanogenic archaea from the rumen and other intestinal environments

Overview

The paper describes the creation of a 16S database specialized for methanogenic archaea.

Background Notes

Technical Details

Overview of the database

Selection of Sequences

Quality control

Sequence Alignment and Phylogenetic Tree Creation

Results

Discussion

The authors stressed that sequencing errors and sequence similarity makes it difficult to delineate certain group. Therefore, they grouped “difficult-to-delineate” sequences together.

Some Notes:

I grabbed this paper to see how other teams (other than SILVA, RDP, Greengenes) are contructing specialized 16S databases. Not being familiar with methanogens, I can’t evaluate how comprehensive their database is. I think that the benchmarking methods could have been improved. The isolate dataset doesn’t reflect a realistic dataset, and few details were provided on the amplicon dataset. Does their database provide superior performance over a range of datasets that methanogen researchers would be interested in? How does it perform on more complex communities? Furthermore, I would be hesitant to use this database for diversity calculations, as it is limited to a small number of organisms, and doesn’t include bacteria.

I liked the inclusion of the analysis of the information content contained in the region of interest of the 16S rRNA gene. It would have liked them to have expanded on this. For example, how does the information content differ between different taxonomic groups? Nonetheless, I’m glad that they mentioned the R tool that they used, as it could be useful for our work. I’m not familar with clone library-based technologies, but they could be worth exploring for inclusion in our database.

Sources

1: seqinR