16S rRNA database for human clinical pathogens?

Question

[Louis Kok]

Hi All, I was wondering if there is any available public 16S rRNA database specific for human bacterial pathogens, other than the generic databases like RDP or SILVA? Thank you.

Answer 1

[natasha.sernova]

Dear Louis,

Wikipedia goes first:

https://en.wikipedia.org/wiki/16S_ribosomal_RNA The authors mention some new databases.

Greengenes Greengenes is a quality controlled, comprehensive 16S reference database and taxonomy based on a de novo phylogeny that provides standard operational taxonomic unit sets. The official home page for the site is http://greengenes.secondgenome.com, and is licensed under the Creative Commons BY-SA 3.0 license.[25][26]

Next - a scientific article describing 16S rRNA and citation from it below. Detection and Identification of Microorganisms by Gene Amplification and Sequencing

http://cid.oxfordjournals.org/content/44/8/1108.full

“The gene target that is most commonly used for bacterial identification is 16S rRNA (or 16S rDNA), an ∼1500 base pair gene that codes for a portion of the 30S ribosome. Partial (500-base pair) 16S rRNA gene sequencing has emerged as a more accurate and faster method to identify a wide variety of aerobic and anaerobic bacteria and has been successfully implemented in clinical laboratories [6–10]. Bacteria may have only a single copy or multiple copies of this gene, and this can make interpretation difficult when base pair changes exist among copies (copy variants). Conversely, multiple copies can be helpful to improve the sensitivity of PCR amplification, especially when applying this technology directly from clinical samples. A major limitation of the 16S rDNA sequence is its inability to discriminate among all bacterial taxa. For example, Bacillus cereus and Bacillus anthracis have identical 16S rDNA sequences and, in fact, cannot be separated reliably at the molecular level by their genomic DNA, because their differences primarily lie in the acquisition of virulence plasmids. For other microorganisms that share complete sequence identity, alternative gene targets can provide better separation of closely related species.”

So 16S rRNA is not a panacea, but scientists still use it. Look at these three papers below. There are really a lot of others, these three are just examples. They are about everything, not only about 16S rRNA.

myPhyloDB: a local web server for the storage and analysis of metagenomic data

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4809264/

MG-RAST, a Metagenomics Service for Analysis of Microbial Community Structure and Function.

http://www.ncbi.nlm.nih.gov/pubmed/26791506

J Clin Bioinforma. 2014 Jan 13;4(1):1. doi: 10.1186/2043-9113-4-1. Clinical detection of human probiotics and human pathogenic bacteria by using a novel high-throughput platform based on next generation sequencing.

http://www.ncbi.nlm.nih.gov/pubmed/24418497

I’ve asked for these topics and searched at NCBI: www.ncbi.nlm.nih.gov

16S rRNA databases AND human clinical pathogens

http://www.ncbi.nlm.nih.gov/pmc/?term=16S%20rRNA%20databases%20AND%20human%20clinical%20pathogens

1700 articles, but just two in a special journal Database.

FusoBase: an online Fusobacterium comparative genomic analysis platform Mia Yang Ang, Hamed Heydari, Nick S. Jakubovics, Mahafizul Imran Mahmud, Avirup Dutta, Wei Yee Wee, Guat Jah Wong, Naresh V.R. Mutha, Shi Yang Tan, Siew Woh Choo Database (Oxford) 2014; 2014: bau082. Published online 2014 August 22. doi: 10.1093/database/bau082

The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information Tsute Chen, Wen-Han Yu, Jacques Izard, Oxana V. Baranova, Abirami Lakshmanan, Floyd E. Dewhirst Database (Oxford) 2010; 2010: baq013. Published online 2010 July 6. doi: 10.1093/database/baq013

[Louis Kok]

Dear Natasha,

Many thanks for the information. This is certainly helpful. :)

Rgds, Louis