BioInformatics, 27 November 2014, Cluj-Napoca, Romania

quality checked and aligned ribosomal RNA sequence data

http://www.arb-silva.de/

Călin G. FLOARE

BioInformatics, 27 November 2014, Cluj-Napoca, Romania

Outline

Why rRNA sequence data

16S rRNA

Silva database

mothur use Silva

Human Microbiome Project (HMP)

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BioInformatics, 27 November 2014, Cluj-Napoca, Romania

Why rRNA sequence data

Sequencing ribosomal RNA (rRNA) genes is currently the method of choice for phylogenetic reconstruction,

nucleic acid based detection and

quantification of microbial diversity.

Ribosomal Database Project (RDP-II)

http://http://rdp.cme.msu.edurdp.cme.msu.eduhttp://www.arbhttp://www.arb--silva.desilva.de//

SILVA quality checked and aligned ribosomal RNA sequence data

rRNA specific databasesrRNA specific databases

SILVA quality checked and aligned ribosomal RNA sequence data

rRNA specific databases

http://www.arbhttp://www.arb--silva.desilva.de//

SILVA quality checked and aligned ribosomal RNA sequence data

rRNA specific databases

http://www.arbhttp://www.arb--silva.desilva.de//

SILVA quality checked and aligned ribosomal RNA sequence data

rRNA specific databases

Ribosomal Database Project (RDP-II)

http://www.arbhttp://www.arb--silva.desilva.de//

SILVA quality checked and aligned ribosomal RNA sequence data

rRNA specific databases

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BioInformatics, 27 November 2014, Cluj-Napoca, Romania

16S ribosomal RNA (or 16S rRNA) is a component of the 30S small subunit of prokaryotic 70S ribosomes.

16S rRNA gene sequencing is considered by current taxonomists to be the gold standard in bacterial identification and classification.

16S rRNA gene contains conserved regions useful for the design of universal PCR primers that can amplify various fragments of the 16S rRNA gene from all pathogenic and nonpathogenic bacteria. These fragments include hypervariable regions containing species-specific signature sequences useful for bacterial identification to species level.

In some instances, alternate genes such as hsp65, rpoB or recA are sequenced when 16S is not adequate for species level identification.

http://http://depts.washington.edu/molmicdx/mdx/tests/bctseq.shtmldepts.washington.edu/molmicdx/mdx/tests/bctseq.shtml

16S rRNA

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16S rRNA

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http://http://rna.ucsc.edu/rnacenter/ribosome_images.htmlrna.ucsc.edu/rnacenter/ribosome_images.html

BioInformatics, 27 November 2014, Cluj-Napoca, Romania

Silva

Silva (from Latin silva, forest), was implemented to provide a central comprehensive up to date web resource of aligned small (16S/18S,SSU) and large (23S/28S, LSU) subunit ribosomal RNA (rRNA) sequences from the Bacteria, Archaea and Eukarya domains.

Release 119 contain full length sequences and taxonomy references for 137879 bacteria, 3155 arches, and 12273 eukarya (~7.2Gb).

All sequences are

checked for anomalies,

carry a rich set of sequence associated contextual information,

have multiple taxonomic classifications, and

contain the latest validly described nomenclature.

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Mothur use Silva

mothur is currently the most cited bioinformatics tool for analyzing 16S rRNA gene sequences

can be used to process data generated by Sanger, PacBio, IonTorrent, 454, and Illumina(MiSeq/HiSeq)

http://http://www.mothur.orgwww.mothur.org

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Mothur is an open-source, platform-independent, community-supported software for describing and comparing microbial communities.

An analysis of 8 marine samples of more than 222,000 16S rRNA gene sequences was completed in less than 2 hours with a laptop computer.

doi: 10.1128/AEM.01541-09

BioInformatics, 27 November 2014, Cluj-Napoca, Romania

Human Microbiome Project (HMP)

Our SelfOur Self--Portrait: the Human Portrait: the Human MicrobiomeMicrobiome

www.nature.com/nature/journal/v486/n7402/www.nature.com/nature/journal/v486/n7402/https://www.broadinstitute.org/news/4199https://www.broadinstitute.org/news/4199

The microbiome are the bacteria living on and within us. Like the rainforest, the healthy human microbiome is a balanced ecosystem. The correct balance of microbes keep potential pathogens in check and regulate the immune system. Microbes also perform essential functions such as digesting food and synthesizing vitamins.

The goal of the Human Microbiome Project is to characterize the human microbiome and analyze its role in human health and disease.

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http://www.hsph.harvard.edu/news/press-releases/human-microbiome-project/files/hmptree_121.pdf

“each person’s microbial signature is fairly unique, in much the same way that an individual’s genome is unique,” Curtis Huttenhower

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Thank you for your attention