title: Sequencing orphan species initiative (SOS): Filling the gaps in the 16S rRNA gene sequence database for all species with validly published names.
abstract: High quality 16S ribosomal RNA (rRNA) gene sequences from the type strains of all species with validly published names, as defined by the International Code of Nomenclature of Bacteria, are a prerequisite for their accurate affiliations within the global genealogical classification and for the recognition of potential new taxa. During the last few years, the Living Tree Project (LTP) has taken care to create a high quality, aligned 16S and 23S rRNA gene sequence database of all type strains. However, the manual curation of the sequence dataset and type strain information revealed that a total of 552 "orphan" species (about 5.7% of the currently classified species) had to be excluded from the reference trees. Among them, 322 type strains were not represented by an SSU entry in the public sequence repositories. The remaining 230 type strains had to be discarded due to bad sequence quality. Since 2010, the LTP team has coordinated a network of researchers and culture collections in order to improve the situation by (re)-sequencing the type strains of these "orphan" species. As a result, we can now report 351 16S rRNA gene sequences of type strains. Nevertheless, 201 species could not be sequenced because cultivable type strains were not available (121), the cultures had either been lost or were never deposited in the first place (66), or it was not possible due to other constraints (14). The International Code of Nomenclature of Bacteria provides a number of mechanisms to deal with the problem of missing type strains and we recommend that due consideration be given to the appropriate mechanisms in order to help solve some of these issues.
authors: Marine Microbiology Group, Department of Ecology and Marine Resources, Institut Mediterráni d'Estudis Avançats, C/Miquel Marqués 21, E-07190 Esporles, Illes Balears, Spain. pyarza@ribocon.com
authors: Pablo
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authors: Yarza
authors: Cathrin
authors: C
authors: Spröer
authors: Jolantha
authors: J
authors: Swiderski
authors: Nicole
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authors: Mrotzek
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authors: Spring
authors: Brian J
authors: BJ
authors: Tindall
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authors: Gronow
authors: Rüdiger
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authors: Pukall
authors: Hans-Peter
authors: HP
authors: Klenk
authors: Elke
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authors: Lang
authors: Susanne
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authors: Verbarg
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authors: Crouch
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authors: Lilburn
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authors: Beck
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authors: Unosson
authors: Sofia
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authors: Cardew
authors: Edward R B
authors: ER
authors: Moore
authors: Margarita
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authors: Gomila
authors: Yasuyoshi
authors: Y
authors: Nakagawa
authors: Danielle
authors: D
authors: Janssens
authors: Paul
authors: P
authors: De Vos
authors: Jindrich
authors: J
authors: Peiren
authors: Timo
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authors: Suttels
authors: Dominique
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authors: Clermont
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authors: Bizet
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authors: Sakamoto
authors: Toshiya
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authors: Iida
authors: Takuji
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authors: Kudo
authors: Yoshimasa
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authors: Kosako
authors: Yumi
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authors: Oshida
authors: Moriya
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authors: Ohkuma
authors: David
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authors: R Arahal
authors: Eva
authors: E
authors: Spieck
authors: Andreas
authors: A
authors: Pommerening Roeser
authors: Marian
authors: M
authors: Figge
authors: Duckchul
authors: D
authors: Park
authors: Peter
authors: P
authors: Buchanan
authors: Ana
authors: A
authors: Cifuentes
authors: Raul
authors: R
authors: Munoz
authors: Jean P
authors: JP
authors: Euzéby
authors: Karl-Heinz
authors: KH
authors: Schleifer
authors: Wolfgang
authors: W
authors: Ludwig
authors: Rudolf
authors: R
authors: Amann
authors: Frank Oliver
authors: FO
authors: Glöckner
authors: Ramon
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authors: Rosselló-Móra
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics*; D002965:Classification / Q000379:methods; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics*; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S