{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,3]],"date-time":"2026-10-03T15:41:55Z","timestamp":1791042115991,"version":"4.1.0"},"reference-count":31,"publisher":"Springer Science and Business Media LLC","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Stand. Genomic Sci."],"published-print":{"date-parts":[[2009,9,23]]},"DOI":"10.4056\/sigs.29547","type":"journal-article","created":{"date-parts":[[2009,10,9]],"date-time":"2009-10-09T23:21:35Z","timestamp":1255130495000},"page":"166-173","source":"Crossref","is-referenced-by-count":33,"title":["Complete genome sequence of Atopobium parvulum type strain (IPP 1246T)"],"prefix":"10.4056","volume":"1","author":[{"given":"Alex","family":"Copeland","sequence":"first","affiliation":[{"name":"1DOE Joint Genome Institute, Walnut Creek, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Johannes","family":"Sikorski","sequence":"additional","affiliation":[{"name":"2DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alla","family":"Lapidus","sequence":"additional","affiliation":[{"name":"1DOE Joint Genome Institute, Walnut Creek, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matt","family":"Nolan","sequence":"additional","affiliation":[{"name":"1DOE Joint Genome Institute, Walnut Creek, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tijana Glavina","family":"Del Rio","sequence":"additional","affiliation":[{"name":"1DOE Joint Genome Institute, Walnut Creek, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susan","family":"Lucas","sequence":"additional","affiliation":[{"name":"1DOE Joint Genome Institute, Walnut Creek, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Feng","family":"Chen","sequence":"additional","affiliation":[{"name":"1DOE Joint Genome Institute, Walnut Creek, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hope","family":"Tice","sequence":"additional","affiliation":[{"name":"1DOE Joint Genome Institute, Walnut Creek, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sam","family":"Pitluck","sequence":"additional","affiliation":[{"name":"1DOE Joint Genome Institute, Walnut Creek, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jan-Fang","family":"Cheng","sequence":"additional","affiliation":[{"name":"1DOE Joint Genome Institute, Walnut Creek, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"R\u00fcdiger","family":"Pukall","sequence":"additional","affiliation":[{"name":"2DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olga","family":"Chertkov","sequence":"additional","affiliation":[{"name":"3Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas","family":"Brettin","sequence":"additional","affiliation":[{"name":"3Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cliff","family":"Han","sequence":"additional","affiliation":[{"name":"3Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John C.","family":"Detter","sequence":"additional","affiliation":[{"name":"3Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cheryl","family":"Kuske","sequence":"additional","affiliation":[{"name":"3Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Bruce","sequence":"additional","affiliation":[{"name":"3Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lynne","family":"Goodwin","sequence":"additional","affiliation":[{"name":"3Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natalia","family":"Ivanova","sequence":"additional","affiliation":[{"name":"1DOE Joint Genome Institute, Walnut Creek, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Konstantinos","family":"Mavromatis","sequence":"additional","affiliation":[{"name":"1DOE Joint Genome Institute, Walnut Creek, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natalia","family":"Mikhailova","sequence":"additional","affiliation":[{"name":"1DOE Joint Genome Institute, Walnut Creek, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amy","family":"Chen","sequence":"additional","affiliation":[{"name":"4Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Krishna","family":"Palaniappan","sequence":"additional","affiliation":[{"name":"4Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patrick","family":"Chain","sequence":"additional","affiliation":[{"name":"5Lawrence Livermore National Laboratory, Livermore, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manfred","family":"Rohde","sequence":"additional","affiliation":[{"name":"6HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Markus","family":"G\u00f6ker","sequence":"additional","affiliation":[{"name":"2DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jim","family":"Bristow","sequence":"additional","affiliation":[{"name":"1DOE Joint Genome Institute, Walnut Creek, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan A.","family":"Eisen","sequence":"additional","affiliation":[{"name":"7University of California Davis Genome Center, Davis, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Victor","family":"Markowitz","sequence":"additional","affiliation":[{"name":"4Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philip","family":"Hugenholtz","sequence":"additional","affiliation":[{"name":"1DOE Joint Genome Institute, Walnut Creek, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nikos C.","family":"Kyrpides","sequence":"additional","affiliation":[{"name":"1DOE Joint Genome Institute, Walnut Creek, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hans-Peter","family":"Klenk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John C.","family":"Detter","sequence":"additional","affiliation":[{"name":"3Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","reference":[{"key":"key20100129142740604_r1"},{"key":"key20100129142740604_r2","first-page":"235","article-title":"Comparative sequence analyses of the 16S rRNA genes of Lactobacillus minutus, Lactobacillus rimae and Streptococcus parvulus: proposal for the creation of a new genus Atopobium.","volume":"74","author":"Collins","year":"1992","journal-title":"FEMS Microbiol Lett"},{"key":"key20100129142740604_r3","doi-asserted-by":"crossref","first-page":"558","DOI":"10.1128\/JCM.41.2.558-563.2003","article-title":"Diversity of bacterial populations on the tongue dorsa of patients with halitosis and healthy patients.","volume":"41","author":"Kazor","year":"2003","journal-title":"J Clin Microbiol"},{"key":"key20100129142740604_r4","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1111\/j.1601-0825.2007.01371.x","article-title":"Molecular identification of bacteria on the tongue dorsum of subjects with and without halitosis.","volume":"14","author":"Riggio","year":"2008","journal-title":"Oral Dis"},{"key":"key20100129142740604_r5","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1177\/154405910308200503","article-title":"New bacterial species associated with chronic periodontitis.","volume":"82","author":"Kumar","year":"2003","journal-title":"J Dent Res"},{"key":"key20100129142740604_r6","doi-asserted-by":"crossref","first-page":"947","DOI":"10.1099\/0022-1317-50-11-947","article-title":"Characterisation of Eubacterium-like strains isolated from oral infections.","volume":"50","author":"Downes","year":"2001","journal-title":"J Med Microbiol"},{"key":"key20100129142740604_r7","doi-asserted-by":"crossref","first-page":"1190","DOI":"10.1126\/science.1171700","article-title":"Topographical and temporal diversity of the human skin microbiome.","volume":"324","author":"Grice","year":"2009","journal-title":"Science"},{"key":"key20100129142740604_r8","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1093\/dnares\/dsm018","article-title":"Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes.","volume":"14","author":"Kurokawa","year":"2007","journal-title":"DNA Res"},{"key":"key20100129142740604_r9","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1126\/science.1093857","article-title":"Environmental genome shotgun sequencing of the Sargasso Sea.","volume":"304","author":"Venter","year":"2004","journal-title":"Science"},{"key":"key20100129142740604_r10","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1093\/oxfordjournals.molbev.a026334","article-title":"Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis.","volume":"17","author":"Castresana","year":"2000","journal-title":"Mol Biol Evol"},{"key":"key20100129142740604_r11","doi-asserted-by":"crossref","first-page":"452","DOI":"10.1093\/bioinformatics\/18.3.452","article-title":"Multiple sequence alignment using partial order graphs.","volume":"18","author":"Lee","year":"2002","journal-title":"Bioinformatics"},{"key":"key20100129142740604_r12","doi-asserted-by":"crossref","first-page":"758","DOI":"10.1080\/10635150802429642","article-title":"A Rapid Bootstrap Algorithm for the RAxML Web Servers.","volume":"57","author":"Stamatakis","year":"2008","journal-title":"Syst Biol"},{"key":"key20100129142740604_r13","doi-asserted-by":"crossref","first-page":"D475","DOI":"10.1093\/nar\/gkm884","article-title":"The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata.","volume":"36","author":"Liolios","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"key20100129142740604_r14","doi-asserted-by":"crossref","first-page":"93","DOI":"10.4056\/sigs.12260","article-title":"Complete genome sequence of Cryptobacterium curtum type strain (12-3T).","volume":"1","author":"Mavrommatis","year":"2009","journal-title":"Stand Genomic Sci"},{"key":"key20100129142740604_r15","doi-asserted-by":"crossref","first-page":"174","DOI":"10.4056\/sigs.33592","article-title":"Complete genome sequence of Eggerthella lenta type strain (IPP VPI 0255T).","volume":"1","author":"Saunders","year":"2009","journal-title":"Stand Genomic Sci"},{"key":"key20100129142740604_r16","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1099\/00207713-41-2-261","article-title":"Lactobacillus uli sp. nov. and Lactobacillus rimae sp. nov. from the human gingival crevice and emended descriptions of Lactobacillus minutus and Streptococcus parvulus.","volume":"41","author":"Olsen","year":"1991","journal-title":"Int J Syst Bacteriol"},{"key":"key20100129142740604_r17","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1099\/00207713-33-1-82","article-title":"Transfer of Peptostreptococcus parvulus (Weinberg, Nativelle, and Pr\u00e9vot 1937) Smith 1957 to the Genus Streptococcus: Streptococcus parvulus (Weinberg, Nativelle, and Pr\u00e9vot 1937) comb, nov., nom. rev., emend.","volume":"33","author":"Cato","year":"1983","journal-title":"Int J Syst Bacteriol"},{"key":"key20100129142740604_r18","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1038\/nbt1360","article-title":"The minimum information about a genome sequence (MIGS) specification.","volume":"26","author":"Field","year":"2008","journal-title":"Nat Biotechnol"},{"key":"key20100129142740604_r19","doi-asserted-by":"crossref","first-page":"4576","DOI":"10.1073\/pnas.87.12.4576","article-title":"Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.","volume":"87","author":"Woese","year":"1990","journal-title":"Proc Natl Acad Sci USA"},{"key":"key20100129142740604_r20"},{"key":"key20100129142740604_r21","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1099\/00207713-47-2-479","article-title":"Proposal for a New Hierarchic Classification System, Actinobacteria classis nov.","volume":"47","author":"Stackebrandt","year":"1997","journal-title":"Int J Syst Bacteriol"},{"key":"key20100129142740604_r22","unstructured":"Anonymous. Biological Agents. Technical rules for biological agents www.baua.de TRBA 466."},{"key":"key20100129142740604_r23","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat Genet"},{"key":"key20100129142740604_r24","doi-asserted-by":"crossref","first-page":"1573","DOI":"10.1099\/00207713-49-4-1573","article-title":"Characterization of a novel Atopobium isolate from the human vagina: description of Atopobium vaginae sp. nov.","volume":"49","author":"Rodriguez Jovita","year":"1999","journal-title":"Int J Syst Bacteriol"},{"key":"key20100129142740604_r25","first-page":"53","article-title":"Cell wall structure of anaerobic cocci.","volume":"14","author":"Weiss","year":"1981","journal-title":"Rev Inst Pasteur Lyon"},{"key":"key20100129142740604_r26","unstructured":"List of media used at DSMZ for cell growth: http:\/\/www.dsmz.de\/microorganisms\/media_list.php"},{"key":"key20100129142740604_r27","doi-asserted-by":"crossref","first-page":"1056","DOI":"10.1038\/nature08656","article-title":"A phylogeny-driven genomic encyclopedia of Bacteria and Archaea.","volume":"462","author":"Wu","year":"2009","journal-title":"Nature"},{"key":"key20100129142740604_r28","doi-asserted-by":"crossref","first-page":"12","DOI":"10.4056\/sigs.761","article-title":"Complete genome of Kytococcus sedentarius type strain (541T).","volume":"1","author":"Sims","year":"2009","journal-title":"Stand Genomic Sci"},{"key":"key20100129142740604_r29","unstructured":"Anonymous. Prodigal Prokaryotic Dynamic Programming Genefinding Algorithm. Oak Ridge National Laboratory and University of Tennessee 2009 http:\/\/compbio.ornl.gov\/prodigal"},{"key":"key20100129142740604_r30"},{"key":"key20100129142740604_r31","doi-asserted-by":"crossref","first-page":"2271","DOI":"10.1093\/bioinformatics\/btp393","article-title":"Expert Review of Functional Annotations for Microbial Genomes.","volume":"25","author":"Markowitz","year":"2009","journal-title":"Bioinformatics"}],"container-title":["Standards in Genomic Sciences"],"original-title":[],"language":"en","deposited":{"date-parts":[[2024,4,9]],"date-time":"2024-04-09T15:54:30Z","timestamp":1712678070000},"score":1,"resource":{"primary":{"URL":"https:\/\/environmentalmicrobiome.biomedcentral.com\/articles\/10.4056\/sigs.29547"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,9,23]]},"references-count":31,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2009,9,23]]}},"alternative-id":["10.4056\/sigs.29547"],"URL":"https:\/\/doi.org\/10.4056\/sigs.29547","relation":{},"ISSN":["1944-3277"],"issn-type":[{"value":"1944-3277","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,9,23]]}}}