{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,25]],"date-time":"2026-03-25T01:59:36Z","timestamp":1774403976972,"version":"3.50.1"},"reference-count":63,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2013,7,18]],"date-time":"2013-07-18T00:00:00Z","timestamp":1374105600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0068648","type":"journal-article","created":{"date-parts":[[2013,7,18]],"date-time":"2013-07-18T22:54:51Z","timestamp":1374188091000},"page":"e68648","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":38,"title":["Prospecting Environmental Mycobacteria: Combined Molecular Approaches Reveal Unprecedented Diversity"],"prefix":"10.1371","volume":"8","author":[{"given":"Alessandra","family":"Pontiroli","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tanya T.","family":"Khera","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Brian B.","family":"Oakley","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sam","family":"Mason","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Scot E.","family":"Dowd","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Emma R.","family":"Travis","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Girum","family":"Erenso","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Abraham","family":"Aseffa","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Orin","family":"Courtenay","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elizabeth M. H.","family":"Wellington","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2013,7,18]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1093\/bmb\/ldq035","article-title":"Nontuberculous mycobacteria: opportunistic environmental pathogens for predisposed hosts","volume":"96","author":"JL Cook","year":"2010","journal-title":"British Medical Bulletin"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1128\/CMR.9.2.177","article-title":"Epidemiology of infection by nontuberculous mycobacteria","volume":"9","author":"JO Falkinham","year":"1996","journal-title":"Clinical Microbiology Reviews"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1007\/s15010-004-4001-4","article-title":"Nontuberculous mycobacterial infections: A clinical review","volume":"32","author":"D Wagner","year":"2004","journal-title":"Infection"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1164\/rccm.200604-571ST","article-title":"An official ATS\/IDSA statement: Diagnosis, treatment, and prevention of nontuberculous mycobacterial diseases","volume":"175","author":"DE Griffith","year":"2007","journal-title":"American Journal of Respiratory and Critical Care Medicine"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1128\/jb.172.1.116-124.1990","article-title":"The division between fast-growing and slow-growing species corresponds to natural relationships among the Mycobacteria","volume":"172","author":"DA Stahl","year":"1990","journal-title":"Journal of Bacteriology"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1023\/A:1023327929535","article-title":"Evidence for phylogenetic inheritance in pathogenicity of <italic>Mycobacterium<\/italic>","volume":"83","author":"MC Leclerc","year":"2003","journal-title":"Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"894","DOI":"10.1111\/j.1469-0691.2009.03011.x","article-title":"Free-living amoebae, a training field for macrophage resistance of mycobacteria","volume":"15","author":"IB Salah","year":"2009","journal-title":"Clinical Microbiology and Infection"},{"key":"ref8","doi-asserted-by":"crossref","unstructured":"Alexander K, Laver P, Michel A, Williams M, van Helden P, et al. (2010 ) Novel Mycobacterium tuberculosis complex pathogen, <italic>M. mungi<\/italic>. Emerg Infect Dis.","DOI":"10.3201\/eid1608.100314"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"1339","DOI":"10.1016\/S0140-6736(95)92348-9","article-title":"Variation in protection by BCG \u2013 implications of and for heterologous immunity","volume":"346","author":"PEM Fine","year":"1995","journal-title":"Lancet"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"5318","DOI":"10.1128\/AEM.68.11.5318-5325.2002","article-title":"Occurrence of mycobacteria in water treatment lines and in water distribution systems","volume":"68","author":"C Le Dantec","year":"2002","journal-title":"Applied and Environmental Microbiology"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"7571","DOI":"10.1128\/AEM.70.12.7571-7573.2004","article-title":"Diversity of nontuberculoid <italic>Mycobacterium<\/italic> species in biofilms of urban and semiurban drinking water distribution systems","volume":"70","author":"SM September","year":"2004","journal-title":"Applied and Environmental Microbiology"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"2492","DOI":"10.1128\/AEM.65.6.2492-2496.1999","article-title":"Occurrence of nontuberculous mycobacteria in environmental samples","volume":"65","author":"TC Covert","year":"1999","journal-title":"Applied and Environmental Microbiology"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1111\/j.1365-2672.2009.04161.x","article-title":"Surrounded by mycobacteria: nontuberculous mycobacteria in the human environment","volume":"107","author":"JO Falkinham","year":"2009","journal-title":"Journal of Applied Microbiology"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"320","DOI":"10.1111\/j.1574-6941.2008.00618.x","article-title":"PCR analysis of the presence and location of <italic>Mycobacterium avium<\/italic> in a constructed reed bed, with implications for avian tuberculosis control","volume":"67","author":"JA Drewe","year":"2009","journal-title":"FEMS Microbiology Ecology"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1016\/j.femsec.2004.04.016","article-title":"Environmental mycobacteria from alpine and subalpine habitats","volume":"49","author":"MF Thorel","year":"2004","journal-title":"FEMS Microbiology Ecology"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1111\/j.1365-2672.1995.tb03113.x","article-title":"Isolation of Mycobacteria from acidic forest soil samples- comparison of culture methods","volume":"78","author":"E Iivanainen","year":"1995","journal-title":"Journal of Applied Bacteriology"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1111\/j.1574-6941.1999.tb00660.x","article-title":"Humic and fulvic acids stimulate the growth of <italic>Mycobacterium avium<\/italic>","volume":"30","author":"RA Kirschner","year":"1999","journal-title":"FEMS Microbiology Ecology"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1046\/j.1365-2672.1999.00711.x","article-title":"Environmental factors affecting the occurrence of mycobacteria in brook sediments","volume":"86","author":"E Iivanainen","year":"1999","journal-title":"Journal of Applied Microbiology"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1016\/j.mimet.2010.04.007","article-title":"Real-time PCR detection of environmental mycobacteria in house dust","volume":"82","author":"E Torvinen","year":"2010","journal-title":"Journal of Microbiological Methods"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"658","DOI":"10.1016\/j.fm.2009.04.005","article-title":"Detection of nontuberculous mycobacteria from water buffalo raw milk in Brazil","volume":"26","author":"CM Jord\u00e3o Junior","year":"2009","journal-title":"Food Microbiology"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"4623","DOI":"10.1128\/AEM.68.9.4623-4628.2002","article-title":"Aquatic Insects as a Vector for <italic>Mycobacterium ulcerans<\/italic>","volume":"68","author":"L Marsollier","year":"2002","journal-title":"Applied and Environmental Microbiology"},{"key":"ref22","first-page":"280","article-title":"Environmental mycobacteria in areas of high and low tuberculosis prevalence in the Islamic Republic of Iran","volume":"12","author":"E Ghaemi","year":"2006","journal-title":"Eastern Mediterranean Health Journal"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"2180","DOI":"10.1128\/AEM.60.6.2180-2183.1994","article-title":"Isolation and identification of Environmental Mycobacteria in the Mycobacterium bovis BCG trial area of south India","volume":"60","author":"T Kamala","year":"1994","journal-title":"Applied and Environmental Microbiology"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"1946","DOI":"10.1128\/AEM.71.4.1946-1952.2005","article-title":"Molecular detection of Mycobacterium bovis and Mycobacterium bovis BCG (Pasteur) in soil","volume":"71","author":"JS Young","year":"2005","journal-title":"Applied and Environmental Microbiology"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"836","DOI":"10.1111\/j.1462-2920.2005.00970.x","article-title":"Distribution of the Mycobacterium community and polycyclic aromatic hydrocarbons (PAHs) among different size fractions of a long-term PAH-contaminated soil","volume":"8","author":"M Uyttebroek","year":"2006","journal-title":"Environmental Microbiology"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1016\/j.femsec.2004.09.015","article-title":"Occurrence and community composition of fast-growing Mycobacterium in soils contaminated with polycyclic aromatic hydrocarbons","volume":"51","author":"NM Leys","year":"2005","journal-title":"FEMS Microbiology Ecology"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1016\/j.soilbio.2010.11.033","article-title":"Environmental mycobacteria closely related to the pathogenic species evidenced in an acidic forest wetland","volume":"43","author":"J Kopecky","year":"2011","journal-title":"Soil Biology & Biochemistry"},{"key":"ref28","first-page":"45","article-title":"Actinobacterial communities of boreal forest soil and lake water are rich in mycobacteria","volume":"11","author":"M Niva","year":"2006","journal-title":"Boreal Environment Research"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1016\/j.mimet.2010.04.007","article-title":"Real-time PCR detection of environmental mycobacteria in house dust","volume":"82","author":"E Torvinen","year":"2010","journal-title":"Journal of Microbiological Methods"},{"key":"ref30","doi-asserted-by":"crossref","unstructured":"Jacobs J, Rhodes M, Sturgis B, Wood B (2009) Influence of Environmental Gradients on the Abundance and Distribution of Mycobacterium spp. in a Coastal Lagoon Estuary. Applied and Environmental Microbiology 75.","DOI":"10.1128\/AEM.01900-09"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1128\/CMR.16.2.319-354.2003","article-title":"Impact of Genotypic Studies on Mycobacterial Taxonomy: the New Mycobacteria of the 1990s","volume":"16","author":"E Tortoli","year":"2003","journal-title":"Clinical Microbiology Reviews"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1186\/1471-2180-8-43","article-title":"Survey of bacterial diversity in chronic wounds using Pyrosequencing, DGGE, and full ribosome shotgun sequencing","volume":"8","author":"S Dowd","year":"2008","journal-title":"BMC Microbiol"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"e17916","DOI":"10.1371\/journal.pone.0017916","article-title":"Pathogen Quantitation in Complex Matrices: A Multi-Operator Comparison of DNA Extraction Methods with a Novel Assessment of PCR Inhibition","volume":"6","author":"A Pontiroli","year":"2011","journal-title":"Plos One"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"7843","DOI":"10.1093\/nar\/17.19.7843","article-title":"Isolation and direct complete nucleotide determination of entire genes: characterization of a gene coding for 16S ribosomal RNA","volume":"17","author":"U Edwards","year":"1989","journal-title":"Nucleic Acids Research"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1016\/j.bbi.2009.12.010","article-title":"Photoperiod modulates gut bacteria composition in male Siberian hamsters (Phodopus sungorus)","volume":"24","author":"MT Bailey","year":"2010","journal-title":"Brain, Behavior, and Immunity"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"7537","DOI":"10.1128\/AEM.01541-09","article-title":"Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities","volume":"75","author":"PD Schloss","year":"2009","journal-title":"Applied and Environmental Microbiology"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"R143","DOI":"10.1186\/gb-2007-8-7-r143","article-title":"Accuracy and quality of massively parallel DNA pyrosequencing","volume":"8","author":"SM Huse","year":"2007","journal-title":"Genome Biolgy"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1111\/j.1462-2920.2009.02051.x","article-title":"Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates","volume":"12","author":"V Kunin","year":"2010","journal-title":"Environmental Microbiology"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"1889","DOI":"10.1111\/j.1462-2920.2010.02193.x","article-title":"Ironing out the wrinkles in the rare biosphere through improved OTU clustering","volume":"12","author":"SM Huse","year":"2010","journal-title":"Environmental Microbiology"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1093\/bioinformatics\/btp636","article-title":"PyNAST: a flexible tool for aligning sequences to a template alignment","volume":"26","author":"JG Caporaso","year":"2010","journal-title":"Bioinformatics"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1038\/nmeth.f.303","article-title":"QIIME allows analysis of high-throughput community sequencing data","volume":"7","author":"JG Caporaso","year":"2010","journal-title":"Nature methods"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"494","DOI":"10.1101\/gr.112730.110","article-title":"Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons","volume":"21","author":"BJ Haas","year":"2011","journal-title":"Genome Research"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"7188","DOI":"10.1093\/nar\/gkm864","article-title":"SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB","volume":"35","author":"E Pruesse","year":"2007","journal-title":"Nucleic Acids Research"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"1658","DOI":"10.1093\/bioinformatics\/btl158","article-title":"Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences","volume":"22","author":"WZ Li","year":"2006","journal-title":"Bioinformatics"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1371\/journal.pone.0008230","article-title":"A High-Throughput DNA Sequence Aligner for Microbial Ecology Studies","volume":"4","author":"PD Schloss","year":"2009","journal-title":"Plos One"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"1363","DOI":"10.1093\/nar\/gkh293","article-title":"ARB: a software environment for sequence data","volume":"32","author":"W Ludwig","year":"2004","journal-title":"Nucleic Acids Research"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"8228","DOI":"10.1128\/AEM.71.12.8228-8235.2005","article-title":"UniFrac: a new phylogenetic method for comparing microbial communities","volume":"71","author":"C Lozupone","year":"2005","journal-title":"Applied and Environmental Microbiology"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1038\/ismej.2009.97","article-title":"Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data","volume":"4","author":"M Hamady","year":"2009","journal-title":"ISME Journal"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"296","DOI":"10.1111\/j.1461-0248.2007.01139.x","article-title":"The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems","volume":"11","author":"MGA Van Der Heijden","year":"2008","journal-title":"Ecology Letters"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1146\/annurev.mi.39.100185.001541","article-title":"Measurement of in Situ Activities of Nonphotosynthetic Microorganisms in Aquatic and Terrestrial Habitats","volume":"39","author":"JT Staley","year":"1985","journal-title":"Annual Review of Microbiology"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"2049","DOI":"10.1099\/ijs.0.64190-0","article-title":"<italic>Mycobacterium colombiense<\/italic> sp. nov., a novel member of the <italic>Mycobacterium avium<\/italic> complex and description of MAC-X as a new ITS genetic variant","volume":"56","author":"MI Murcia","year":"2006","journal-title":"International Journal of Systematic and Evolutionary Microbiology"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1128\/JCM.01536-09","article-title":"Commercial DNA Probes for Mycobacteria Incorrectly Identify a Number of Less Frequently Encountered Species","volume":"48","author":"E Tortoli","year":"2010","journal-title":"Journal of Clinical Microbiology"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1023\/A:1000669317571","article-title":"Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology","volume":"73","author":"G Muyzer","year":"1998","journal-title":"Antonie van Leeuwenhoek"},{"key":"ref54","doi-asserted-by":"crossref","unstructured":"Calvo-Bado LA, Oakley BB, Dowd SE, Green LE, Medley GF, <etal>et al<\/etal>.. (2011) Ovine pedomics: the first study of the ovine foot 16S rRNA-based microbiome. ISME Journal.","DOI":"10.1038\/ismej.2011.25"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"5555","DOI":"10.1111\/j.1365-294X.2010.04898.x","article-title":"Quantifying microbial communities with 454 pyrosequencing: does read abundance count?","volume":"19","author":"AS Amend","year":"2010","journal-title":"Molecular Ecology"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"668","DOI":"10.1038\/nmeth0910-668b","article-title":"Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions","volume":"7","author":"J Reeder","year":"2010","journal-title":"Nature Methods"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1099\/00207713-40-4-323","article-title":"Towards a Phylogeny and Definition of Species at the Molecular Level within the Genus Mycobacterium","volume":"40","author":"T Rogall","year":"1990","journal-title":"International Journal of Systematic Bacteriology"},{"key":"ref58","first-page":"1043","article-title":"Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology","volume":"52","author":"E Stackebrandt","year":"2002","journal-title":"International Journal of Systematic and Evolutionary Microbiology"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1099\/ijs.0.63222-0","article-title":"A multigene approach to phylogenetic analysis using the genus Mycobacterium as a model","volume":"55","author":"G Devulder","year":"2005","journal-title":"International Journal of Systematic and Evolutionary Microbiology"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"1432","DOI":"10.1099\/ijs.0.65658-0","article-title":"A seven-gene, multilocus, genus-wide approach to the phylogeny of mycobacteria using supertrees","volume":"58","author":"S Mignard","year":"2008","journal-title":"International Journal of Systematic and Evolutionary Microbiology"},{"key":"ref61","first-page":"2092","article-title":"Comparison of DNA Pyrosequencing with Alternative Methods for Identification of Mycobacteria. Journal of Clinical Microbiology","volume":"46","author":"LC Heller","year":"2008"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1038\/nature11234","article-title":"Structure, function and diversity of the healthy human microbiome","volume":"486","year":"2012","journal-title":"Nature"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"e47075","DOI":"10.1371\/journal.pone.0047075","article-title":"Species-Level Analysis of DNA Sequence Data from the NIH Human Microbiome Project","volume":"7","author":"S Conlan","year":"2012","journal-title":"PLoS ONE"}],"container-title":["PLoS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0068648","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,7,31]],"date-time":"2020-07-31T05:43:05Z","timestamp":1596174185000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0068648"}},"subtitle":[],"editor":[{"given":"Yoshihiko","family":"Hoshino","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2013,7,18]]},"references-count":63,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2013,7,18]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0068648","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,7,18]]}}}