2,339
Views
26
CrossRef citations to date
0
Altmetric
Original Articles

Metataxonomics reveal vultures as a reservoir for Clostridium perfringens

, , , , , , , , , , & show all
Pages 1-8 | Received 25 Sep 2016, Accepted 12 Dec 2016, Published online: 15 Jan 2019

References

  • Woolhouse M, Gaunt E.Ecological origins of novel human pathogens. Crit Rev Microbiol 2007;33: 231–242.
  • Mazet JA, Wei Q, Zhao G Jet al.Joint China-US call for employing a transdisciplinary approach to emerging infectious diseases. Ecohealth 2015;12: 555–559.
  • Kahn RE, Clouser DF, Richt JA.Emerging infections: a tribute to the one medicine, one health concept. Zoonoses Public Health 2009;56: 407–428.
  • Lu X, Ke D, Zeng X, Gong G, Ci R.Status, ecology, and conservation of the Himalayan griffon Gyps himalayensis (Aves, Accipitridae) in the Tibetan plateau. Ambio 2009;38: 166–173.
  • Ge P, Xi J, Ding Jet al.Primary case of human pneumonic plague occurring in a Himalayan marmot natural focus area Gansu Province, China. Int J Infect Dis 2015;33: 67–70.
  • Marchesi JR, Ravel J.The vocabulary of microbiome research: a proposal. Microbiome 2015;3: 31.
  • Yarza P, Yilmaz P, Pruesse Eet al.Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 2014;12: 635–645.
  • Schloss PD, Jenior ML, Koumpouras CC, Westcott SL, Highlander SK.Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system. PeerJ 2016;4: e1869.
  • Mora-Ruiz MR, Font-Verdera F, Orfila A, Rita J, Rossello-Mora R.Endophytic microbial diversity of the halophyte Arthrocnemum macrostachyum across plant compartments. FEMS Microbiol Ecol 2016;92: fiw145.
  • Vidal R, Ginard D, Khorrami Set al.Crohn associated microbial communities associated to colonic mucosal biopsies in patients of the western Mediterranean. Syst Appl Microbiol 2015;38: 442–452.
  • Seibold I, Helbig AJ.Evolutionary history of New and Old World vultures inferred from nucleotide sequences of the mitochondrial cytochrome b gene. Philos Trans R Soc Lond B Biol Sci 1995;350: 163–178.
  • Kerr KCR, Stoeckle MY, Dove CJ, Weigt LA, Francis CM.Hebert PDN. Comprehensive DNA barcode coverage of North American birds. Mol Ecol Notes 2007;7: 535–543.
  • Weisburg WG, Barns SM, Pelletier DA, Lane DJ.16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991;173: 697–703.
  • Klindworth A, Pruesse E, Schweer Tet al.Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res 2013;41: e1.
  • Magoc T, Salzberg SL.FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 2011;27: 2957–2963.
  • Bokulich NA, Subramanian S, Faith JJet al.Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods 2013;10: 57–59.
  • Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R.UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 2011;27: 2194–2200.
  • Wang Q, Garrity GM, Tiedje JM, Cole JR.Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 2007;73: 5261–5267.
  • Hammer Ø, Harper DA, Ryan PD.PAST: paleontological statistics software package for education and data analysis. Palaeontol Electr 2001;4: 1–9.
  • Edgar RC.UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 2013;10: 996–998.
  • Yarza P, Ludwig W, Euzeby Jet al.Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses. Syst Appl Microbiol 2010;33: 291–299.
  • Quast C, Pruesse E, Yilmaz Pet al.The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 2013;41: D590–D596.
  • Ludwig W, Strunk O, Westram Ret al.ARB: a software environment for sequence data. Nucleic Acids Res 2004;32: 1363–1371.
  • Munoz R, Yarza P, Rosselló-Móra R.Harmonized phylogenetic trees for the Prokaryotes.In: Rosenberg E, DeLong EF, Stackebrandt E, Thompson F (eds). The Prokaryotes: Actinobacteria.Springer-Verlag Berlin Heidelberg.2014, 1–3.
  • Roggenbuck M, Baerholm Schnell I, Blom Net al.The microbiome of New World vultures. Nat Commun 2014;5: 5498.
  • Mora-Ruiz MR, Font-Verdera F, Diaz-Gil Cet al.Moderate halophilic bacteria colonizing the phylloplane of halophytes of the subfamily Salicornioideae (Amaranthaceae). Syst Appl Microbiol 2015;38: 406–416.
  • Jost BH, Trinh HT, Songer JG.Clonal relationships among Clostridium perfringens of porcine origin as determined by multilocus sequence typing. Vet Microbiol 2006;116: 158–165.
  • Baums CG, Schotte U, Amtsberg G, Goethe R.Diagnostic multiplex PCR for toxin genotyping of Clostridium perfringens isolates. Vet Microbiol 2004;100: 11–16.
  • Chalmers G, Bruce HL, Hunter DBet al.Multilocus sequence typing analysis of Clostridium perfringens isolates from necrotic enteritis outbreaks in broiler chicken populations. J Clin Microbiol 2008;46: 3957–3964.
  • Lebreton F, Willems RJL, Gilmore MS.Enterococcus diversity, origins in nature, and gut colonization.In: Gilmore MS, Clewell DB, Ike Y, Shankar N (eds). Enterococci: From Commensals to Leading Causes of Drug Resistant Infection [Internet]. Boston: Massachusetts Eye and Ear Infirmary, 2014.
  • Woo PC, Teng JL, Yeung JM, Tse H, Lau SK, Yuen KY.Automated identification of medically important bacteria by 16S rRNA gene sequencing using a novel comprehensive database, 16SpathDB. J Clin Microbiol 2011;49: 1799–1809.
  • Silva RO, Lobato FC.Clostridium perfringens: A review of enteric diseases in dogs, cats and wild animals. Anaerobe 2015;33: 14–17.
  • Goldstein MR, Kruth SA, Bersenas AM, Holowaychuk MK, Weese JS.Detection and characterization of Clostridium perfringens in the feces of healthy and diarrheic dogs. Can J Vet Res 2012;76: 161–165.
  • Rooney AP, Swezey JL, Friedman R, Hecht DW, Maddox CW.Analysis of core housekeeping and virulence genes reveals cryptic lineages of Clostridium perfringens that are associated with distinct disease presentations. Genetics 2006;172: 2081–2092.
  • Scallan E, Hoekstra RM, Angulo FJet al.Foodborne illness acquired in the United States—major pathogens. Emerg Infect Dis 2011;17: 7–15.
  • Li J, Sayeed S, McClane BA.Prevalence of Enterotoxigenic Clostridium perfringens Isolates in Pittsburgh (Pennsylvania) Area Soils and Home Kitchens. Appl Environ Microbiol 2007;73: 7218–7224.
  • Baumgardner DJ.Soil-related bacterial and fungal infections. J Am Board Fam Med 2012;25: 734–744.
  • Ryan MP, Pembroke JT, Adley CC.Genotypic and phenotypic diversity of Ralstonia pickettii and Ralstonia insidiosa isolates from clinical and environmental sources including High-purity Water. Diversity in Ralstonia pickettii. BMC Microbiol 2011;11: 194.
  • Labarca JA, Trick WE, Peterson CLet al.Multistate nosocomial outbreak of Ralstonia pickettii colonization associated with an intrinsically contaminated respiratory care solution. Clin Infect Dis 1999;29: 1281–1286.
  • Coppotelli BM, Ibarrolaza A, Del Panno MT, Morelli IS.Effects of the inoculant strain Sphingomonas paucimobilis 20006FA on soil bacterial community and biodegradation in phenanthrene-contaminated soil. Microb Ecol 2007;55: 173–183.