lpsn—list of prokaryotic names with standing in nomenclature
TRANSCRIPT
LPSNmdashlist of prokaryotic names with standingin nomenclatureAidan C Parte
LPSN 261 Willis Road Sudbury MA 01776 USA
Received September 30 2013 Accepted October 21 2013
ABSTRACT
The List of Prokaryotic Names with Standing inNomenclature (LPSN httpwwwbacterionet) is adatabase that lists the names of prokaryotes(Bacteria and Archaea) that have been validly pub-lished in the International Journal of Systematic andEvolutionary Microbiology directly or by inclusion ina Validation List under the Rules of InternationalCode of Nomenclature of Bacteria Currently thereare 15 974 taxa listed In addition LPSN hasan up-to-date classification of prokaryotes andinformation on prokaryotic nomenclature andculture collections
INTRODUCTION
The List of Prokaryotic Names with Standing inNomenclature (LPSN) available at httpwwwbacterionet was established in 1997 as the of List of BacterialNames with Standing in Nomenclature (LBSN) whichwas available for downloading via an FTP server (1) Itsubsequently was published online on 28 January 1998and has been updated with the publication of each issueof the International Journal of Systematic and Bacteriology(IJSB) renamed International Journal of Systematic andEvolutionary Microbiology (IJSEM) in 2000 LPSN wasfounded and curated by Prof Jean Euzeby EcoleNationale Veterinaire de Toulouse Toulouse Franceuntil his retirement in June 2013 (2) Having collaboratedwith Prof Euzeby and been a heavy user of LPSN over theyears in my roles as Managing Editor of IJSB IJSEM andBergeyrsquos Manual of Systematic Bacteriology he entrustedLPSN to me on his retirement Prof Euzebyrsquos interest andexpertise in systematic bacteriology and Latin and Greekand his fastidious updates to LPSN have made it the mostauthoritative source for prokaryotic nomenclature Hiswork has also been facilitated by his close collaborationwith IJSEMrsquos editorial board and staff
Each year the number of new validly published namesincreases In 2000 370 new names were validly publishedThis increased to 804 in 2007 As of August 842 new
names were published in 2013 (Table 1) This rapidincrease in validly published names illustrates theproblem in keeping up with changes in prokaryotic no-menclature By providing accurate information aboutthe current status of a name synonyms and other usefulinformation LPSN is a solution to this problem
WHAT IS A VALIDLY PUBLISHED NAME
Although there is no official classification of prokaryotestheir names are governed by the International Code ofNomenclature of Bacteria (aka the Bacteriological Code)an official publication of the International Committee onSystematics of Prokaryotes (ICSP) formerly theInternational Committee on Systematic Bacteriology(ICSB) The Bacteriological Code contains GeneralConsiderations Principles Rules and Recommendationson the naming of prokaryotes The Bacteriological Codegoverns names of prokaryotes in the ranks of ClassSubclass Order Suborder Family Subfamily TribeSubtribe Genus Subgenus Species and SubspeciesTaxa above the rank of Class (Phylum KingdomDivision and Domain) are not covered by the CodeIn 1975 the Bacteriological Code (1975 Revision)
introduced the concept of lsquovalid publicationrsquo of names ofprokaryotes The rationale for this action was largely toreduce the number of redundant ambiguous andconfusing names in common use The publication of theApproved Lists of Bacterial Names (3) was part of thisconcept and set a new starting point in prokaryoticnomenclature The Approved Lists of Bacterial Namescontain 2212 names of genera species or subspecies and124 names of higher taxa (family and above) lsquoThe namesare only approved in the sense that they were approved forretention in the new bacteriological nomenclaturersquo (4)The International Code of Nomenclature of Bacteria
(1990 Revision) is the cornerstone of prokaryotic nomen-clature (5) It states that the name of a taxon is validlypublished and therefore has standing in nomenclature ifone of the following criteria is met (i) The name is cited inthe Approved Lists of Bacterial Names (ii) The name ispublished in papers in the IJSB or in the IJSEM andconforms to requirements laid down in the
To whom correspondence should be addressed Tel +1 978 443 2820 Email aidanpartegmailcom
Published online 15 November 2013 Nucleic Acids Research 2014 Vol 42 Database issue D613ndashD616doi101093nargkt1111
The Author(s) 2013 Published by Oxford University PressThis is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (httpcreativecommonsorglicensesby-nc30) which permits non-commercial re-use distribution and reproduction in any medium provided the original work is properly cited For commercialre-use please contact journalspermissionsoupcom
Bacteriological Code (iii) The name is validly published byannouncement in a Validation List Validation Lists arelists published in the IJSBIJSEM validating prokaryoticnames effectively but not validly publishedAnnouncement in a Validation List is the responsibility
of the author of the name or new combinationmdashauthorswishing to submit new names andor combinations forinclusion in a list must send appropriate documentationto the IJSEM Editorial Office or to the Lists EditorFollowing the Paris meeting of the ICSP in August2002 it is also a requirement that authors of newspecies new subspecies and new combinations providedocumentary evidence that type strains are deposited inat least two recognized culture collections in two differentcountries (ie documents certifying deposition and avail-ability of type strains) and are available from those culturecollections without restrictionsAccording to the above criteria LPSN lists all validly
published names of prokaryotes from the Approved Listsand culled from IJSBIJSEM and its Validation Lists Italso includes listings of some non-valid names Candidatustaxa (taxa which have been incompletely described and donot meet the requirements for valid publication)
endangered prokaryotic names (type strains having onlybeen deposited in a single culture collection) and taxaabove the rank of class Every taxon of rank genus orhigher has its own pagemdash2950 at present and thereare 150 additional pages of classifications indices etc
STRUCTURE OF A TYPICAL TAXON ENTRYIN LPSN
Figure 1 is a screenshot of a typical entry for a speciesin LPSN in this case Fictibacillus arsenicus comb novThe first line gives the species name in purple as thisis a new combination formed by the reclassificationof Bacillus arsenicus the authority or reference forthe original name or basonym (Shivaji et al 2005) isgiven in parentheses followed by the authority for thepresent classification Glaeser et al 2013 This isfollowed by the taxon status in this case comb nov(for combinatio nova)
The next line gives the type strain and collection strainnumbers assigned to the type strain preceded inparentheses by the hyperlink to StrainInfonet which isan integrated microbial knowledge base developed at
Table 1 Names validly published since the Approved Lists of Bacterial Names up to 1 August 2013
Year Taxonomic rank Annual total
Class Subclass Order Suborder Family Genus Species Subspecies
1980 0 0 0 0 2 10 49 1 621981 0 0 3 0 5 22 103 7 1401982 0 0 1 0 3 16 102 13 1351983 0 0 0 0 2 27 166 17 2121984 0 0 1 0 4 31 161 23 2201985 0 0 0 0 0 29 125 14 1681986 0 0 1 0 3 27 176 16 2231987 0 0 2 0 2 19 100 11 1341988 5 0 1 0 1 30 144 8 1891989 0 0 2 0 5 23 167 19 2161990 0 0 0 0 3 21 148 30 2021991 0 0 0 0 5 21 145 12 1831992 0 0 0 0 1 0 122 16 1391993 0 0 1 0 2 36 178 6 2231994 0 0 0 0 0 42 161 6 2091995 0 0 1 0 2 37 217 11 2681996 0 0 1 0 3 46 232 20 3021997 1 5 6 10 19 42 223 4 3101998 1 0 0 0 1 55 256 6 3191999 0 0 0 0 4 79 273 14 3702000 0 0 0 0 8 76 275 11 3702001 0 0 0 0 1 68 356 8 4332002 42 0 25 0 14 72 350 9 5122003 1 0 1 0 3 75 372 20 4722004 0 0 3 0 13 80 435 13 5442005 1 0 12 0 20 105 528 6 6722006 6 0 19 1 38 118 593 4 7792007 3 0 5 3 8 135 631 19 8042008 1 0 5 0 11 116 597 8 7382009 2 0 7 2 12 112 663 15 8132010 7 1 9 0 25 105 611 13 7712011 2 0 3 1 11 105 619 13 7542012 9 0 8 0 26 100 655 11 8092013a 16 0 9 4 14 121 666 12 842Total 97 6 126 21 271 2001 10 599 416 13 537
aUp to the August issue of IJSEM
D614 Nucleic Acids Research 2014 Vol 42 Database issue
Ghent University (6) The GenBank sequence accessionnumber for the 16S rRNA gene of the type strain isprovided and hyperlinked The basonym of the speciesis given and a link to its entry in LPSN is provided viathe curren symbol The etymology or derivation of the name islisted where known The source of isolation of the typestrain is given for all new species or subspecies publishedor validated from the July 2013 issue onwards of IJSEMfollowed by the reference to the published article inIJSEM with a hyperlink via the articlersquos DOI [For taxathat appear on a Validation List references to the List andthe effective publication again with hyperlinks via the Listand article DOIs are provided when possible]
CLASSIFICATION
There is no official classification of prokaryotes as this isa matter of scientific judgment and general agreement (4)The most widely accepted classification is the lsquoTaxonomicOutline of the Prokaryotesrsquo initiated in the early 1990s inthe editorial office of Bergeyrsquos Manual Trust as a prelim-inary step in organizing the content of the second editionof Bergeyrsquos Manual of Systematic Bacteriology
The classification used in the LPSN is based on theoriginal publications andor the latest lsquoTaxonomicOutline of the Bacteria and Archaearsquo (httpwwwtaxonomicoutlineorg) (7) andor the lsquoNCBI TaxonomyBrowserrsquo (httpwwwncbinlmnihgovTaxonomyBrowserwwwtaxcgimode=Root) andor TaxonomicOutlines for Volumes 3 and 4 of Bergeyrsquos Manual ofSystematic Bacteriology (Second Edition) (8) (9) andorlsquoThe All-Species Living Tree Projectrsquo (10) This classifica-tion is subject to revision following examination of large-scale phylogenetic models
Since taxa above the rank of class are not covered bythe Rules of the Bacteriological Code such names cannotbe validly published and they are cited in quotes forexample the phylum lsquoEuryarchaeotarsquo in Figure 2 Eachtaxon entry in the classifications links to the individualtaxon page
SITE STATISTICS
The use of LPSN rose steadily from its inception to a peakin 2007 of 18 million visits (Table 2) As of 2012 it wasgetting 12 million visits a year Currently there are nostatistics monitoring on the site
Table 2 Web server statistics for 2003ndash12a
Year Visitsb Pagesc
2003 700 500 2 496 1062004 859 902 3 484 6002005 1 252 369 5 945 0882006 1 780 511 7 231 4872007 1 810 513 5 544 5092008 1 419 144 6 532 1902009 1 406 178 5 581 1392010 1 566 970 6 193 6192011 1 239 165 4 434 0262012 1 249 629 4 080 135
aStatstics generated by Webalizer In addition to LPSN Prof Euzebywas also the author of a website entitled lsquoDictionnaire de BacteriologieVeterinairersquo To avoid additional web hosting fees lsquoDictionnaire deBacteriologie Veterinairersquo was included as a folder in LPSN So thestatistics given in Table 2 encompass the results of both sitesbVisits occur when some remote site makes a request for a page on theserver for the first time As long as the same site keeps making requestswithin a given timeout period they will all be considered part of thesame Visit If the site makes a request to the server and the length oftime since the last request is greater than the specified timeout period(30 min) a new Visit is started and counted and the sequence repeatsSince only pages will trigger a visit remotes sites that link to graphicand other non-page URLs will not be counted in the visit totalsreducing the number of false visitsAdditional information Whenever a request is made to the server from agiven IP address (site) the amount of time since a previous request bythe address is calculated (if any) If the time difference is greater than apre-configured lsquovisit timeoutrsquo value (or has never made a requestbefore) it is considered a lsquonew visitrsquo and this total is incremented(both for the site and the IP address) The timeout value is 30 minso if a user visits the site at 100 in the afternoon and then returns at300 two visits would be registeredcPages are those URLs that would be considered the actual page beingrequested and not all of the individual items that make it up (such asgraphics)
Figure 1 Screenshot of a typical entry for a species in LPSN
Figure 2 Screenshot of part of the classification of the domainArchaea
Nucleic Acids Research 2014 Vol 42 Database issue D615
SEARCH ENGINE
A Google Custom Search Engine was added to the fixednavigation bar for easy access from any position onevery page of the site Indexing requests are submittedto Google via a sitemapxml file following the additionof new taxa files
NEW DEVELOPMENTS AND PLANS
After Prof Euzebyrsquos final updates to the site following pub-lication of the June issue of IJSEM the LPSN was recodedand reformatted using CSS to enable streamlining of theHTML code and to facilitate updates On 30 June 2013 thesite was re-launched on a new server at gandinet underthe URL httpwwwbacterionet The names publishedor validated in the July and August issues of IJSEM havebeen added using a FileMaker Pro database to calculate theHTML The data for the FileMaker database are importedafter manipulating in Word and Excel citations down-loaded from PubMed into Endnote and files supplied bythe SGM the publisher of IJSEM Calculated HTML isthen added to existing files or new files are created as ne-cessary for example when a new genus is addedIn order to make the site more useful the source of
type strains has been added for each new species orsubspecies where available Current categories areEnvironmental Environmentalmdashsoil Environmentalmdashfreshwater Environmentalmdashmarine Human ClinicalAnimal Veterinary Oral Plant Plant pathogenIndustrial and FoodIn addition to the StrainInfonet link I plan to add links
from the type strain designations directly to the majorculture collections (such as DSMZ ATCC LMG JCMand KCTC) in order to facilitate ordering strains from thecollections LPSN will be developed to work properly onsmartphones and tablets in the near future The Webalizerweb server log file analysis program will be reinstated onLPSN in due course
ACKNOWLEDGEMENTS
The author would like to thank Barny Whitman forconstructive comments on this article Jean Euzeby forgiving me LPSN without restrictions or interferenceand Susan Andrews (SGM) and Robin Dunford fortheir support
FUNDING
Currently LPSN is self-funded (as it was by my predeces-sor) but will accept (and solicit) appropriate sponsors
and grants in the future Advertising has been added onthe search results page via the Google AdSense systemthus far negligible revenue has been generated TheSGM has supplied a complimentary online subscriptionto IJSEM Online which has been an invaluableresource Funding for open access charge Waived byOxford University Press
Conflict of interest statement None declared
REFERENCES
1 EuzebyJP (1997) List of bacterial names with standing innomenclature a folder available on the internet Int J SystBacteriol 47 590ndash592
2 OrenA and GarrityG (2013) Retirement of ProfessorJean Paul Euzeby as list editor Int J Syst Evol Microbiol 632373
3 SkermanVBD McGowanV and SneathPHA (1980) Approvedlists of bacterial names Int J Syst Bacteriol 30 225ndash420
4 SneathPHA and BrennerDJ (1992) lsquolsquoOfficialrsquorsquo nomenclaturelists ASM News 58 175
5 LapageSP SneathPHA LesselEF SkermanVBDSeeligerHPR and ClarkWA (1992) International Code ofNomenclature of Bacteria (1990 Revision) Bacteriological CodePublished for IUMS by the American Society for MicrobiologyWashington DC
6 DawyndtP VancanneytM De MeyerH and SwingsJ (2005)Knowledge accumulation and resolution of data inconsistenciesduring the integration of microbial information sources IEEETrans Knowl Data Eng 17 1111ndash1126
7 GarrityGM LilburnTG ColeJR HarrisonSH EuzebyJand TindallBJ (2007) Taxonomic Outline of the Bacteriaand Archaea Release 77 Michigan State University Boardof Trustees httpdxdoiorg (29 October 2013 date lastaccessed)
8 LudwigW SchleiferK-H and WhitmanWB (2009) Taxonomicoutline of the phylum Firmicutes In De VosP GarrityGMJonesD KriegNR LudwigW RaineyFA SchleiferK-Hand WhitmanWB (eds) Bergeyrsquos Manual of SystematicBacteriology Vol 3 The Firmicutes 2nd edn Springer NewYork pp 15ndash17
9 LudwigW EuzebyJ and WhitmanWB (2009) Taxonomicoutline of the phyla Bacteroidetes Spirochaetes Tenericutes(Mollicutes) Acidobacteria Fibrobacteres FusobacteriaDictyoglomi Gemmatimonadetes Lentisphaerae VerrucomicrobiaChlamydiae and Planctomycetes In KriegNR StaleyJTHedlundB PasterBJ WardN LudwigW and WhitmanWB(eds) Bergeyrsquos Manual of Systematic Bacteriology 2nd ednVol 4 The Bacteroidetes Spirochaetes Tenericutes (Mollicutes)Acidobacteria Fibrobacteres Fusobacteria DictyoglomiGemmatimonadetes Lentisphaerae Verrucomicrobia Chlamydiaeand Planctomycetes Springer New York pp 21ndash24
10 YarzaP RichterM PepliesJ EuzebyJ AmannRSchleiferKH LudwigW GlocknerFO and Rossello-MoraR(2008) The All-Species Living Tree project a 16S rRNA-basedphylogenetic tree of all sequenced type strains Syst ApplMicrobiol 31 241ndash250
D616 Nucleic Acids Research 2014 Vol 42 Database issue
Bacteriological Code (iii) The name is validly published byannouncement in a Validation List Validation Lists arelists published in the IJSBIJSEM validating prokaryoticnames effectively but not validly publishedAnnouncement in a Validation List is the responsibility
of the author of the name or new combinationmdashauthorswishing to submit new names andor combinations forinclusion in a list must send appropriate documentationto the IJSEM Editorial Office or to the Lists EditorFollowing the Paris meeting of the ICSP in August2002 it is also a requirement that authors of newspecies new subspecies and new combinations providedocumentary evidence that type strains are deposited inat least two recognized culture collections in two differentcountries (ie documents certifying deposition and avail-ability of type strains) and are available from those culturecollections without restrictionsAccording to the above criteria LPSN lists all validly
published names of prokaryotes from the Approved Listsand culled from IJSBIJSEM and its Validation Lists Italso includes listings of some non-valid names Candidatustaxa (taxa which have been incompletely described and donot meet the requirements for valid publication)
endangered prokaryotic names (type strains having onlybeen deposited in a single culture collection) and taxaabove the rank of class Every taxon of rank genus orhigher has its own pagemdash2950 at present and thereare 150 additional pages of classifications indices etc
STRUCTURE OF A TYPICAL TAXON ENTRYIN LPSN
Figure 1 is a screenshot of a typical entry for a speciesin LPSN in this case Fictibacillus arsenicus comb novThe first line gives the species name in purple as thisis a new combination formed by the reclassificationof Bacillus arsenicus the authority or reference forthe original name or basonym (Shivaji et al 2005) isgiven in parentheses followed by the authority for thepresent classification Glaeser et al 2013 This isfollowed by the taxon status in this case comb nov(for combinatio nova)
The next line gives the type strain and collection strainnumbers assigned to the type strain preceded inparentheses by the hyperlink to StrainInfonet which isan integrated microbial knowledge base developed at
Table 1 Names validly published since the Approved Lists of Bacterial Names up to 1 August 2013
Year Taxonomic rank Annual total
Class Subclass Order Suborder Family Genus Species Subspecies
1980 0 0 0 0 2 10 49 1 621981 0 0 3 0 5 22 103 7 1401982 0 0 1 0 3 16 102 13 1351983 0 0 0 0 2 27 166 17 2121984 0 0 1 0 4 31 161 23 2201985 0 0 0 0 0 29 125 14 1681986 0 0 1 0 3 27 176 16 2231987 0 0 2 0 2 19 100 11 1341988 5 0 1 0 1 30 144 8 1891989 0 0 2 0 5 23 167 19 2161990 0 0 0 0 3 21 148 30 2021991 0 0 0 0 5 21 145 12 1831992 0 0 0 0 1 0 122 16 1391993 0 0 1 0 2 36 178 6 2231994 0 0 0 0 0 42 161 6 2091995 0 0 1 0 2 37 217 11 2681996 0 0 1 0 3 46 232 20 3021997 1 5 6 10 19 42 223 4 3101998 1 0 0 0 1 55 256 6 3191999 0 0 0 0 4 79 273 14 3702000 0 0 0 0 8 76 275 11 3702001 0 0 0 0 1 68 356 8 4332002 42 0 25 0 14 72 350 9 5122003 1 0 1 0 3 75 372 20 4722004 0 0 3 0 13 80 435 13 5442005 1 0 12 0 20 105 528 6 6722006 6 0 19 1 38 118 593 4 7792007 3 0 5 3 8 135 631 19 8042008 1 0 5 0 11 116 597 8 7382009 2 0 7 2 12 112 663 15 8132010 7 1 9 0 25 105 611 13 7712011 2 0 3 1 11 105 619 13 7542012 9 0 8 0 26 100 655 11 8092013a 16 0 9 4 14 121 666 12 842Total 97 6 126 21 271 2001 10 599 416 13 537
aUp to the August issue of IJSEM
D614 Nucleic Acids Research 2014 Vol 42 Database issue
Ghent University (6) The GenBank sequence accessionnumber for the 16S rRNA gene of the type strain isprovided and hyperlinked The basonym of the speciesis given and a link to its entry in LPSN is provided viathe curren symbol The etymology or derivation of the name islisted where known The source of isolation of the typestrain is given for all new species or subspecies publishedor validated from the July 2013 issue onwards of IJSEMfollowed by the reference to the published article inIJSEM with a hyperlink via the articlersquos DOI [For taxathat appear on a Validation List references to the List andthe effective publication again with hyperlinks via the Listand article DOIs are provided when possible]
CLASSIFICATION
There is no official classification of prokaryotes as this isa matter of scientific judgment and general agreement (4)The most widely accepted classification is the lsquoTaxonomicOutline of the Prokaryotesrsquo initiated in the early 1990s inthe editorial office of Bergeyrsquos Manual Trust as a prelim-inary step in organizing the content of the second editionof Bergeyrsquos Manual of Systematic Bacteriology
The classification used in the LPSN is based on theoriginal publications andor the latest lsquoTaxonomicOutline of the Bacteria and Archaearsquo (httpwwwtaxonomicoutlineorg) (7) andor the lsquoNCBI TaxonomyBrowserrsquo (httpwwwncbinlmnihgovTaxonomyBrowserwwwtaxcgimode=Root) andor TaxonomicOutlines for Volumes 3 and 4 of Bergeyrsquos Manual ofSystematic Bacteriology (Second Edition) (8) (9) andorlsquoThe All-Species Living Tree Projectrsquo (10) This classifica-tion is subject to revision following examination of large-scale phylogenetic models
Since taxa above the rank of class are not covered bythe Rules of the Bacteriological Code such names cannotbe validly published and they are cited in quotes forexample the phylum lsquoEuryarchaeotarsquo in Figure 2 Eachtaxon entry in the classifications links to the individualtaxon page
SITE STATISTICS
The use of LPSN rose steadily from its inception to a peakin 2007 of 18 million visits (Table 2) As of 2012 it wasgetting 12 million visits a year Currently there are nostatistics monitoring on the site
Table 2 Web server statistics for 2003ndash12a
Year Visitsb Pagesc
2003 700 500 2 496 1062004 859 902 3 484 6002005 1 252 369 5 945 0882006 1 780 511 7 231 4872007 1 810 513 5 544 5092008 1 419 144 6 532 1902009 1 406 178 5 581 1392010 1 566 970 6 193 6192011 1 239 165 4 434 0262012 1 249 629 4 080 135
aStatstics generated by Webalizer In addition to LPSN Prof Euzebywas also the author of a website entitled lsquoDictionnaire de BacteriologieVeterinairersquo To avoid additional web hosting fees lsquoDictionnaire deBacteriologie Veterinairersquo was included as a folder in LPSN So thestatistics given in Table 2 encompass the results of both sitesbVisits occur when some remote site makes a request for a page on theserver for the first time As long as the same site keeps making requestswithin a given timeout period they will all be considered part of thesame Visit If the site makes a request to the server and the length oftime since the last request is greater than the specified timeout period(30 min) a new Visit is started and counted and the sequence repeatsSince only pages will trigger a visit remotes sites that link to graphicand other non-page URLs will not be counted in the visit totalsreducing the number of false visitsAdditional information Whenever a request is made to the server from agiven IP address (site) the amount of time since a previous request bythe address is calculated (if any) If the time difference is greater than apre-configured lsquovisit timeoutrsquo value (or has never made a requestbefore) it is considered a lsquonew visitrsquo and this total is incremented(both for the site and the IP address) The timeout value is 30 minso if a user visits the site at 100 in the afternoon and then returns at300 two visits would be registeredcPages are those URLs that would be considered the actual page beingrequested and not all of the individual items that make it up (such asgraphics)
Figure 1 Screenshot of a typical entry for a species in LPSN
Figure 2 Screenshot of part of the classification of the domainArchaea
Nucleic Acids Research 2014 Vol 42 Database issue D615
SEARCH ENGINE
A Google Custom Search Engine was added to the fixednavigation bar for easy access from any position onevery page of the site Indexing requests are submittedto Google via a sitemapxml file following the additionof new taxa files
NEW DEVELOPMENTS AND PLANS
After Prof Euzebyrsquos final updates to the site following pub-lication of the June issue of IJSEM the LPSN was recodedand reformatted using CSS to enable streamlining of theHTML code and to facilitate updates On 30 June 2013 thesite was re-launched on a new server at gandinet underthe URL httpwwwbacterionet The names publishedor validated in the July and August issues of IJSEM havebeen added using a FileMaker Pro database to calculate theHTML The data for the FileMaker database are importedafter manipulating in Word and Excel citations down-loaded from PubMed into Endnote and files supplied bythe SGM the publisher of IJSEM Calculated HTML isthen added to existing files or new files are created as ne-cessary for example when a new genus is addedIn order to make the site more useful the source of
type strains has been added for each new species orsubspecies where available Current categories areEnvironmental Environmentalmdashsoil Environmentalmdashfreshwater Environmentalmdashmarine Human ClinicalAnimal Veterinary Oral Plant Plant pathogenIndustrial and FoodIn addition to the StrainInfonet link I plan to add links
from the type strain designations directly to the majorculture collections (such as DSMZ ATCC LMG JCMand KCTC) in order to facilitate ordering strains from thecollections LPSN will be developed to work properly onsmartphones and tablets in the near future The Webalizerweb server log file analysis program will be reinstated onLPSN in due course
ACKNOWLEDGEMENTS
The author would like to thank Barny Whitman forconstructive comments on this article Jean Euzeby forgiving me LPSN without restrictions or interferenceand Susan Andrews (SGM) and Robin Dunford fortheir support
FUNDING
Currently LPSN is self-funded (as it was by my predeces-sor) but will accept (and solicit) appropriate sponsors
and grants in the future Advertising has been added onthe search results page via the Google AdSense systemthus far negligible revenue has been generated TheSGM has supplied a complimentary online subscriptionto IJSEM Online which has been an invaluableresource Funding for open access charge Waived byOxford University Press
Conflict of interest statement None declared
REFERENCES
1 EuzebyJP (1997) List of bacterial names with standing innomenclature a folder available on the internet Int J SystBacteriol 47 590ndash592
2 OrenA and GarrityG (2013) Retirement of ProfessorJean Paul Euzeby as list editor Int J Syst Evol Microbiol 632373
3 SkermanVBD McGowanV and SneathPHA (1980) Approvedlists of bacterial names Int J Syst Bacteriol 30 225ndash420
4 SneathPHA and BrennerDJ (1992) lsquolsquoOfficialrsquorsquo nomenclaturelists ASM News 58 175
5 LapageSP SneathPHA LesselEF SkermanVBDSeeligerHPR and ClarkWA (1992) International Code ofNomenclature of Bacteria (1990 Revision) Bacteriological CodePublished for IUMS by the American Society for MicrobiologyWashington DC
6 DawyndtP VancanneytM De MeyerH and SwingsJ (2005)Knowledge accumulation and resolution of data inconsistenciesduring the integration of microbial information sources IEEETrans Knowl Data Eng 17 1111ndash1126
7 GarrityGM LilburnTG ColeJR HarrisonSH EuzebyJand TindallBJ (2007) Taxonomic Outline of the Bacteriaand Archaea Release 77 Michigan State University Boardof Trustees httpdxdoiorg (29 October 2013 date lastaccessed)
8 LudwigW SchleiferK-H and WhitmanWB (2009) Taxonomicoutline of the phylum Firmicutes In De VosP GarrityGMJonesD KriegNR LudwigW RaineyFA SchleiferK-Hand WhitmanWB (eds) Bergeyrsquos Manual of SystematicBacteriology Vol 3 The Firmicutes 2nd edn Springer NewYork pp 15ndash17
9 LudwigW EuzebyJ and WhitmanWB (2009) Taxonomicoutline of the phyla Bacteroidetes Spirochaetes Tenericutes(Mollicutes) Acidobacteria Fibrobacteres FusobacteriaDictyoglomi Gemmatimonadetes Lentisphaerae VerrucomicrobiaChlamydiae and Planctomycetes In KriegNR StaleyJTHedlundB PasterBJ WardN LudwigW and WhitmanWB(eds) Bergeyrsquos Manual of Systematic Bacteriology 2nd ednVol 4 The Bacteroidetes Spirochaetes Tenericutes (Mollicutes)Acidobacteria Fibrobacteres Fusobacteria DictyoglomiGemmatimonadetes Lentisphaerae Verrucomicrobia Chlamydiaeand Planctomycetes Springer New York pp 21ndash24
10 YarzaP RichterM PepliesJ EuzebyJ AmannRSchleiferKH LudwigW GlocknerFO and Rossello-MoraR(2008) The All-Species Living Tree project a 16S rRNA-basedphylogenetic tree of all sequenced type strains Syst ApplMicrobiol 31 241ndash250
D616 Nucleic Acids Research 2014 Vol 42 Database issue
Ghent University (6) The GenBank sequence accessionnumber for the 16S rRNA gene of the type strain isprovided and hyperlinked The basonym of the speciesis given and a link to its entry in LPSN is provided viathe curren symbol The etymology or derivation of the name islisted where known The source of isolation of the typestrain is given for all new species or subspecies publishedor validated from the July 2013 issue onwards of IJSEMfollowed by the reference to the published article inIJSEM with a hyperlink via the articlersquos DOI [For taxathat appear on a Validation List references to the List andthe effective publication again with hyperlinks via the Listand article DOIs are provided when possible]
CLASSIFICATION
There is no official classification of prokaryotes as this isa matter of scientific judgment and general agreement (4)The most widely accepted classification is the lsquoTaxonomicOutline of the Prokaryotesrsquo initiated in the early 1990s inthe editorial office of Bergeyrsquos Manual Trust as a prelim-inary step in organizing the content of the second editionof Bergeyrsquos Manual of Systematic Bacteriology
The classification used in the LPSN is based on theoriginal publications andor the latest lsquoTaxonomicOutline of the Bacteria and Archaearsquo (httpwwwtaxonomicoutlineorg) (7) andor the lsquoNCBI TaxonomyBrowserrsquo (httpwwwncbinlmnihgovTaxonomyBrowserwwwtaxcgimode=Root) andor TaxonomicOutlines for Volumes 3 and 4 of Bergeyrsquos Manual ofSystematic Bacteriology (Second Edition) (8) (9) andorlsquoThe All-Species Living Tree Projectrsquo (10) This classifica-tion is subject to revision following examination of large-scale phylogenetic models
Since taxa above the rank of class are not covered bythe Rules of the Bacteriological Code such names cannotbe validly published and they are cited in quotes forexample the phylum lsquoEuryarchaeotarsquo in Figure 2 Eachtaxon entry in the classifications links to the individualtaxon page
SITE STATISTICS
The use of LPSN rose steadily from its inception to a peakin 2007 of 18 million visits (Table 2) As of 2012 it wasgetting 12 million visits a year Currently there are nostatistics monitoring on the site
Table 2 Web server statistics for 2003ndash12a
Year Visitsb Pagesc
2003 700 500 2 496 1062004 859 902 3 484 6002005 1 252 369 5 945 0882006 1 780 511 7 231 4872007 1 810 513 5 544 5092008 1 419 144 6 532 1902009 1 406 178 5 581 1392010 1 566 970 6 193 6192011 1 239 165 4 434 0262012 1 249 629 4 080 135
aStatstics generated by Webalizer In addition to LPSN Prof Euzebywas also the author of a website entitled lsquoDictionnaire de BacteriologieVeterinairersquo To avoid additional web hosting fees lsquoDictionnaire deBacteriologie Veterinairersquo was included as a folder in LPSN So thestatistics given in Table 2 encompass the results of both sitesbVisits occur when some remote site makes a request for a page on theserver for the first time As long as the same site keeps making requestswithin a given timeout period they will all be considered part of thesame Visit If the site makes a request to the server and the length oftime since the last request is greater than the specified timeout period(30 min) a new Visit is started and counted and the sequence repeatsSince only pages will trigger a visit remotes sites that link to graphicand other non-page URLs will not be counted in the visit totalsreducing the number of false visitsAdditional information Whenever a request is made to the server from agiven IP address (site) the amount of time since a previous request bythe address is calculated (if any) If the time difference is greater than apre-configured lsquovisit timeoutrsquo value (or has never made a requestbefore) it is considered a lsquonew visitrsquo and this total is incremented(both for the site and the IP address) The timeout value is 30 minso if a user visits the site at 100 in the afternoon and then returns at300 two visits would be registeredcPages are those URLs that would be considered the actual page beingrequested and not all of the individual items that make it up (such asgraphics)
Figure 1 Screenshot of a typical entry for a species in LPSN
Figure 2 Screenshot of part of the classification of the domainArchaea
Nucleic Acids Research 2014 Vol 42 Database issue D615
SEARCH ENGINE
A Google Custom Search Engine was added to the fixednavigation bar for easy access from any position onevery page of the site Indexing requests are submittedto Google via a sitemapxml file following the additionof new taxa files
NEW DEVELOPMENTS AND PLANS
After Prof Euzebyrsquos final updates to the site following pub-lication of the June issue of IJSEM the LPSN was recodedand reformatted using CSS to enable streamlining of theHTML code and to facilitate updates On 30 June 2013 thesite was re-launched on a new server at gandinet underthe URL httpwwwbacterionet The names publishedor validated in the July and August issues of IJSEM havebeen added using a FileMaker Pro database to calculate theHTML The data for the FileMaker database are importedafter manipulating in Word and Excel citations down-loaded from PubMed into Endnote and files supplied bythe SGM the publisher of IJSEM Calculated HTML isthen added to existing files or new files are created as ne-cessary for example when a new genus is addedIn order to make the site more useful the source of
type strains has been added for each new species orsubspecies where available Current categories areEnvironmental Environmentalmdashsoil Environmentalmdashfreshwater Environmentalmdashmarine Human ClinicalAnimal Veterinary Oral Plant Plant pathogenIndustrial and FoodIn addition to the StrainInfonet link I plan to add links
from the type strain designations directly to the majorculture collections (such as DSMZ ATCC LMG JCMand KCTC) in order to facilitate ordering strains from thecollections LPSN will be developed to work properly onsmartphones and tablets in the near future The Webalizerweb server log file analysis program will be reinstated onLPSN in due course
ACKNOWLEDGEMENTS
The author would like to thank Barny Whitman forconstructive comments on this article Jean Euzeby forgiving me LPSN without restrictions or interferenceand Susan Andrews (SGM) and Robin Dunford fortheir support
FUNDING
Currently LPSN is self-funded (as it was by my predeces-sor) but will accept (and solicit) appropriate sponsors
and grants in the future Advertising has been added onthe search results page via the Google AdSense systemthus far negligible revenue has been generated TheSGM has supplied a complimentary online subscriptionto IJSEM Online which has been an invaluableresource Funding for open access charge Waived byOxford University Press
Conflict of interest statement None declared
REFERENCES
1 EuzebyJP (1997) List of bacterial names with standing innomenclature a folder available on the internet Int J SystBacteriol 47 590ndash592
2 OrenA and GarrityG (2013) Retirement of ProfessorJean Paul Euzeby as list editor Int J Syst Evol Microbiol 632373
3 SkermanVBD McGowanV and SneathPHA (1980) Approvedlists of bacterial names Int J Syst Bacteriol 30 225ndash420
4 SneathPHA and BrennerDJ (1992) lsquolsquoOfficialrsquorsquo nomenclaturelists ASM News 58 175
5 LapageSP SneathPHA LesselEF SkermanVBDSeeligerHPR and ClarkWA (1992) International Code ofNomenclature of Bacteria (1990 Revision) Bacteriological CodePublished for IUMS by the American Society for MicrobiologyWashington DC
6 DawyndtP VancanneytM De MeyerH and SwingsJ (2005)Knowledge accumulation and resolution of data inconsistenciesduring the integration of microbial information sources IEEETrans Knowl Data Eng 17 1111ndash1126
7 GarrityGM LilburnTG ColeJR HarrisonSH EuzebyJand TindallBJ (2007) Taxonomic Outline of the Bacteriaand Archaea Release 77 Michigan State University Boardof Trustees httpdxdoiorg (29 October 2013 date lastaccessed)
8 LudwigW SchleiferK-H and WhitmanWB (2009) Taxonomicoutline of the phylum Firmicutes In De VosP GarrityGMJonesD KriegNR LudwigW RaineyFA SchleiferK-Hand WhitmanWB (eds) Bergeyrsquos Manual of SystematicBacteriology Vol 3 The Firmicutes 2nd edn Springer NewYork pp 15ndash17
9 LudwigW EuzebyJ and WhitmanWB (2009) Taxonomicoutline of the phyla Bacteroidetes Spirochaetes Tenericutes(Mollicutes) Acidobacteria Fibrobacteres FusobacteriaDictyoglomi Gemmatimonadetes Lentisphaerae VerrucomicrobiaChlamydiae and Planctomycetes In KriegNR StaleyJTHedlundB PasterBJ WardN LudwigW and WhitmanWB(eds) Bergeyrsquos Manual of Systematic Bacteriology 2nd ednVol 4 The Bacteroidetes Spirochaetes Tenericutes (Mollicutes)Acidobacteria Fibrobacteres Fusobacteria DictyoglomiGemmatimonadetes Lentisphaerae Verrucomicrobia Chlamydiaeand Planctomycetes Springer New York pp 21ndash24
10 YarzaP RichterM PepliesJ EuzebyJ AmannRSchleiferKH LudwigW GlocknerFO and Rossello-MoraR(2008) The All-Species Living Tree project a 16S rRNA-basedphylogenetic tree of all sequenced type strains Syst ApplMicrobiol 31 241ndash250
D616 Nucleic Acids Research 2014 Vol 42 Database issue
SEARCH ENGINE
A Google Custom Search Engine was added to the fixednavigation bar for easy access from any position onevery page of the site Indexing requests are submittedto Google via a sitemapxml file following the additionof new taxa files
NEW DEVELOPMENTS AND PLANS
After Prof Euzebyrsquos final updates to the site following pub-lication of the June issue of IJSEM the LPSN was recodedand reformatted using CSS to enable streamlining of theHTML code and to facilitate updates On 30 June 2013 thesite was re-launched on a new server at gandinet underthe URL httpwwwbacterionet The names publishedor validated in the July and August issues of IJSEM havebeen added using a FileMaker Pro database to calculate theHTML The data for the FileMaker database are importedafter manipulating in Word and Excel citations down-loaded from PubMed into Endnote and files supplied bythe SGM the publisher of IJSEM Calculated HTML isthen added to existing files or new files are created as ne-cessary for example when a new genus is addedIn order to make the site more useful the source of
type strains has been added for each new species orsubspecies where available Current categories areEnvironmental Environmentalmdashsoil Environmentalmdashfreshwater Environmentalmdashmarine Human ClinicalAnimal Veterinary Oral Plant Plant pathogenIndustrial and FoodIn addition to the StrainInfonet link I plan to add links
from the type strain designations directly to the majorculture collections (such as DSMZ ATCC LMG JCMand KCTC) in order to facilitate ordering strains from thecollections LPSN will be developed to work properly onsmartphones and tablets in the near future The Webalizerweb server log file analysis program will be reinstated onLPSN in due course
ACKNOWLEDGEMENTS
The author would like to thank Barny Whitman forconstructive comments on this article Jean Euzeby forgiving me LPSN without restrictions or interferenceand Susan Andrews (SGM) and Robin Dunford fortheir support
FUNDING
Currently LPSN is self-funded (as it was by my predeces-sor) but will accept (and solicit) appropriate sponsors
and grants in the future Advertising has been added onthe search results page via the Google AdSense systemthus far negligible revenue has been generated TheSGM has supplied a complimentary online subscriptionto IJSEM Online which has been an invaluableresource Funding for open access charge Waived byOxford University Press
Conflict of interest statement None declared
REFERENCES
1 EuzebyJP (1997) List of bacterial names with standing innomenclature a folder available on the internet Int J SystBacteriol 47 590ndash592
2 OrenA and GarrityG (2013) Retirement of ProfessorJean Paul Euzeby as list editor Int J Syst Evol Microbiol 632373
3 SkermanVBD McGowanV and SneathPHA (1980) Approvedlists of bacterial names Int J Syst Bacteriol 30 225ndash420
4 SneathPHA and BrennerDJ (1992) lsquolsquoOfficialrsquorsquo nomenclaturelists ASM News 58 175
5 LapageSP SneathPHA LesselEF SkermanVBDSeeligerHPR and ClarkWA (1992) International Code ofNomenclature of Bacteria (1990 Revision) Bacteriological CodePublished for IUMS by the American Society for MicrobiologyWashington DC
6 DawyndtP VancanneytM De MeyerH and SwingsJ (2005)Knowledge accumulation and resolution of data inconsistenciesduring the integration of microbial information sources IEEETrans Knowl Data Eng 17 1111ndash1126
7 GarrityGM LilburnTG ColeJR HarrisonSH EuzebyJand TindallBJ (2007) Taxonomic Outline of the Bacteriaand Archaea Release 77 Michigan State University Boardof Trustees httpdxdoiorg (29 October 2013 date lastaccessed)
8 LudwigW SchleiferK-H and WhitmanWB (2009) Taxonomicoutline of the phylum Firmicutes In De VosP GarrityGMJonesD KriegNR LudwigW RaineyFA SchleiferK-Hand WhitmanWB (eds) Bergeyrsquos Manual of SystematicBacteriology Vol 3 The Firmicutes 2nd edn Springer NewYork pp 15ndash17
9 LudwigW EuzebyJ and WhitmanWB (2009) Taxonomicoutline of the phyla Bacteroidetes Spirochaetes Tenericutes(Mollicutes) Acidobacteria Fibrobacteres FusobacteriaDictyoglomi Gemmatimonadetes Lentisphaerae VerrucomicrobiaChlamydiae and Planctomycetes In KriegNR StaleyJTHedlundB PasterBJ WardN LudwigW and WhitmanWB(eds) Bergeyrsquos Manual of Systematic Bacteriology 2nd ednVol 4 The Bacteroidetes Spirochaetes Tenericutes (Mollicutes)Acidobacteria Fibrobacteres Fusobacteria DictyoglomiGemmatimonadetes Lentisphaerae Verrucomicrobia Chlamydiaeand Planctomycetes Springer New York pp 21ndash24
10 YarzaP RichterM PepliesJ EuzebyJ AmannRSchleiferKH LudwigW GlocknerFO and Rossello-MoraR(2008) The All-Species Living Tree project a 16S rRNA-basedphylogenetic tree of all sequenced type strains Syst ApplMicrobiol 31 241ndash250
D616 Nucleic Acids Research 2014 Vol 42 Database issue