A short presentation about Silva rRNA database. Silva provides comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya).

1. quality checked and aligned ribosomal RNA sequence data
Călin G. FLOARE
 http://www.arb-silva.de/
BioInformatics, 27 November 2014, Cluj-Napoca, Romania

2. Outline
BioInformatics, 27 November 2014, Cluj-Napoca, Romania
 Why rRNA sequence data
 16S rRNA
 Silva database
 mothur use Silva
 Human Microbiome Project (HMP)
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3. 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)
rrRRNNAA ssppeecciiffiicc ddaattaabbaasseess
rRNA specific databases
hhttttpp::////wwwwww..aarrbb--ssiillvvaa..ddee//
hhttttpp::////rrddpp..ccmmee..mmssuu..eedduu
BioInformatics, 27 November 2014, Cluj-Napoca, Romania
SILVA quality checked and aligned
ribosomal RNA sequence data
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4. 16S rRNA
 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.
hhttttpp::////ddeeppttss..wwaasshhiinnggttoonn..eedduu//mmoollmmiiccddxx//mmddxx//tteessttss//bbccttsseeqq..sshhttmmll
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5. 16S rRNA
hhttttpp::////rrnnaa..uuccsscc..eedduu//rrnnaacceenntteerr//rriibboossoommee__iimmaaggeess..hhttmmll
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6. 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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17. BioInformatics, 27 November 2014, Cluj-Napoca, Romania
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)
hhttttpp::////wwwwww..mmootthhuurr..oorrgg
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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

18. Human Microbiome Project (HMP)
 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.
OOuurr SSeellff--PPoorrttrraaiitt:: tthhee HHuummaann MMiiccrroobbiioommee
wwwwww..nnaattuurree..ccoomm//nnaattuurree//jjoouurrnnaall//vv448866//nn77440022//
hhttttppss::////wwwwww..bbrrooaaddiinnssttiittuuttee..oorrgg//nneewwss//44119999
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19.  “each person’s microbial signature is fairly unique, in much the same way
that an individual’s genome is unique,” Curtis Huttenhower
http://www.hsph.harvard.edu/news/press-releases/human-microbiome-project/files/hmptree_121.pdf
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20. Thank you for your attention
BioInformatics, 27 November 2014, Cluj-Napoca, Romania