Sequencing orphan species initiative (SOS): Filling the gaps in the 16S rRNA gene sequence database for all species with validly published names

被引：62

作者：

Yarza, Pablo ^{[1
,19
]}

Sproeer, Cathrin ^{[2
]}

Swiderski, Jolantha ^{[2
]}

Mrotzek, Nicole ^{[2
]}

Spring, Stefan ^{[2
]}

Tindall, Brian J. ^{[2
]}

Gronow, Sabine ^{[2
]}

Pukall, Ruediger ^{[2
]}

Klenk, Hans-Peter ^{[2
]}

Lang, Elke ^{[2
]}

Verbarg, Susanne ^{[2
]}

Crouch, Audra ^{[3
]}

Lilburn, Timothy ^{[3
]}

Beck, Brian ^{[3
]}

Unosson, Christel ^{[4
]}

Cardew, Sofia ^{[4
]}

Moore, Edward R. B. ^{[4
]}

Gomila, Margarita ^{[5
]}

Nakagawa, Yasuyoshi ^{[6
]}

Janssens, Danielle ^{[7
]}

De Vos, Paul ^{[7
]}

Peiren, Jindrich ^{[7
]}

Suttels, Timo ^{[7
]}

Clermont, Dominique ^{[8
]}

Bizet, Chantal ^{[8
]}

Sakamoto, Mitsuo ^{[9
]}

Iida, Toshiya ^{[9
]}

Kudo, Takuji ^{[9
]}

Kosako, Yoshimasa ^{[9
]}

Oshida, Yumi ^{[9
]}

Ohkuma, Moriya ^{[9
]}

Arahal, David R. ^{[10
]}

Spieck, Eva ^{[11
]}

Roeser, Andreas Pommerening ^{[11
]}

Figge, Marian ^{[12
]}

Park, Duckchul ^{[13
]}

Buchanan, Peter ^{[13
]}

Cifuentes, Ana ^{[1
]}

Munoz, Raul ^{[1
]}

Euzeby, Jean P. ^{[14
,15
]}

Schleifer, Karl-Heinz ^{[16
]}

Ludwig, Wolfgang ^{[16
]}

Amann, Rudolf ^{[17
]}

Gloeckner, Frank Oliver ^{[17
,18
]}

Rossello-Mora, Ramon ^{[1
]}

机构：

[1] Inst Mediterrani Estudis Avancats CSIC UIB, Marine Microbiol Grp, Dept Ecol & Marine Resources, E-07190 Esporles, Illes Balears, Spain

[2] Leibniz Inst DSMZ German Collect Microorganisms &, D-38124 Braunschweig, Germany

[3] ATCC, Manassas, VA 20110 USA

[4] Univ Gothenburg, CCUG, Sahlgrenska Acad, SE-41346 Gothenburg, Sweden

[5] Hosp Son Llatzer, Palma de Mallorca 07198, Islas Baleares, Spain

[6] Natl Inst Technol & Evaluat, NBRC Biol Resource Ctr NBRC, Dept Biotechnol, Kisarazu, Chiba 2920818, Japan

[7] Univ Ghent, BCCM LMG Belgian Coordinated Collect Microorganis, B-9000 Ghent, Belgium

[8] Collect Inst Pasteur, CIP Inst Pasteur, Dept Microbiol, F-75015 Paris, France

[9] RIKEN BioResource Ctr, JCM, Tsukuba, Ibaraki 3050074, Japan

[10] Univ Valencia, CECT, Dept Microbiol & Ecol, E-46980 Valencia, Spain

[11] Univ Hamburg, BZF Bioctr Klein Flottbek, D-22609 Hamburg, Germany

[12] CBS KNAW Fungal Biodivers Ctr, NCCB, NL-3508 Utrecht, Netherlands

[13] Landcare Res, ICMP, Auckland 1072, New Zealand

[14] SBSV, F-31076 Toulouse 03, France

[15] ENVT, F-31076 Toulouse 03, France

[16] Tech Univ Munich, Lehrstuhl Mikrobiol, D-85350 Freising Weihenstephan, Germany

[17] Max Plank Inst Marine Microbiol, D-28359 Bremen, Germany

[18] Jacobs Univ Bremen, D-28759 Bremen, Germany

[19] Ribocon GmbH, D-28359 Bremen, Germany

来源：

SYSTEMATIC AND APPLIED MICROBIOLOGY | 2013年 / 36卷 / 01期

关键词：

Microbial taxonomy; Archaea/bacteria classification/genetics; 16S ribosomal RNA; Orphan species; Type strain; Culture collection; LIVING TREE PROJECT; BACTERIOLOGICAL CODE; PROPOSAL; FLAVOBACTERIUM; BACTERIA; STRAINS; REQUEST; RULES;

D O I：

10.1016/j.syapm.2012.12.006

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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 351 165 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. (C) 2013 Elsevier GmbH. All rights reserved.

引用

页码：69 / 73

页数：5

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