Erratum: Expression of Concern: Plant and Fungal Diversity in Gut Microbiota as Revealed by Molecular and Culture Investigations (PLoS ONE (2013) 8:3 (e59474) DOI: 10.1371/journal.pone.0059474);Plant and Fungal Diversity in Gut Microbiota as Revealed by Molecular and Culture Investigations

PLoS ONE

Volumn 8, Issue 3, 2013, Pages

  Gouba, Nina ^a   Raoult, Didier ^a   Drancourt, Michel ^a  

^a AIX MARSEILLE UNIVERSITÉ   (France)

Author keywords

[No Author keywords available]

Indexed keywords

INTERNAL TRANSCRIBED SPACER; RNA 18S;

ADULT; ANGELICA ANOMALA; ARTICLE; ASPERGILLUS FLAVIPES; ATRACTYLODES JAPONICA; BASIDIOMYCETES; BEAUVERIA BASSIANA; BODY MASS; CAUCASIAN; CHLOROPLAST GENE; CHYTRIDIOMYCETES; CONTROLLED STUDY; DIATOM; FECES ANALYSIS; FEMALE; FIBRAUREA TINCTORIA; FRANCE; FUNGUS; FUNGUS CULTURE; FUNGUS IDENTIFICATION; GENE SEQUENCE; HUMAN; HUMAN TISSUE; INTESTINE FLORA; ISARIA FARINOSA; MEDICINAL PLANT; MICROBIAL DIVERSITY; MITELLA NUDA; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; OBESITY; PENICILLIUM BREVICOMPACTUM; PENICILLIUM CAMEMBERTI; PENICILLIUM DIPODOMYICOLA; POLYMERASE CHAIN REACTION; SPECIES DIVERSITY; STREPTOPHYTA; UNINDEXED SEQUENCE;

EID: 84875028824     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0278014     Document Type: Erratum

References (64)

1. Tilg H, Moschen AR, Kaser A, (2009) Obesity and the microbiota. Gastroenterology 136: 1476-1483.
2. Backhed F, (2011) Programming of host metabolism by the gut microbiota. Ann Nutr Metab 58Suppl 2: 44-52.
3. Backhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI, (2005) Host-bacterial mutualism in the human intestine. Science 307: 1915-1920.
4. Tsai F, Coyle WJ, (2009) The microbiome and obesity: is obesity linked to our gut flora? Curr Gastroenterol Rep 11: 307-313.
5. Ley RE, (2010) Obesity and the human microbiome. Curr Opin Gastroenterol 26: 5-11.
6. DiBaise JK, Zhang H, Crowell MD, Krajmalnik-Brown R, Decker GA, et al. (2008) Gut microbiota and its possible relationship with obesity. Mayo Clin Proc 83: 460-469.
7. Million M, Maraninchi M, Henry M, Armougom F, Richet H, et al. (2011) Obesity-associated gut microbiota is enriched in Lactobacillus reuteri and depleted in Bifidobacterium animalis and Methanobrevibacter smithii. Int J Obes Lond 36: 817-825.
8. Rajilic-Stojanovic M, Smidt H, de Vos WM, (2007) Diversity of the human gastrointestinal tract microbiota revisited. Environ Microbiol 9: 2125-2136.
9. Scanlan PD, Marchesi JR, (2008) Micro-eukaryotic diversity of the human distal gut microbiota: qualitative assessment using culture-dependent and-independent analysis of faeces. ISME J 2: 1183-1193.
10. Nam YD, Chang HW, Kim KH, Roh SW, Kim MS, et al. (2008) Bacterial, archaeal, and eukaryal diversity in the intestines of Korean people. J Microbiol 46: 491-501.
11. Ott SJ, Kuhbacher T, Musfeldt M, Rosenstiel P, Hellmig S, et al. (2008) Fungi and inflammatory bowel diseases: Alterations of composition and diversity. Scand J Gastroenterol 43: 831-841.
12. Chen Y, Chen Z, Guo R, Chen N, Lu H, et al. (2011) Correlation between gastrointestinal fungi and varying degrees of chronic hepatitis B virus infection. Diagn Microbiol Infect Dis 70: 492-498.
13. Li Q, Wang C, Zhang Q, Tang C, Li N, et al. (2012) Use of 18S ribosomal DNA polymerase chain reaction-denaturing gradient gel electrophoresis to study composition of fungal community in 2 patients with intestinal transplants. Hum Pathol 43: 1273-1281.
14. Fredricks DN, Smith C, Meier A, (2005) Comparison of Six DNA Extraction Methods for Recovery of Fungal DNA as Assessed by Quantitative PCR. J. Clin Microbiol 43(10): 5122-5128.
15. Griffiths LJ, Anyim M, Doffman SR, Wilks M, Millar MR, et al. (2006) Comparison of DNA extraction methods for Aspergillus fumigatus using real-time PCR. J Med Microbiol 55 (9): 1187-1191.
16. Poinar HN, Kuch M, Sobolik KD, Barnes I, Stankiewicz AB, et al. (2001) A molecular analysis of dietary diversity for three archaic Native Americans. Proc Natl Acad Sci U S A 98: 4317-4322.
17. Stensvold CR, Lebbad M, Verweij JJ, (2011) The impact of genetic diversity in protozoa on molecular diagnostics. Trends Parasitol 27: 53-58.
18. Slapeta J, Moreira D, Lopez-Garcia P, (2005) The extent of protist diversity: insights from molecular ecology of freshwater eukaryotes. Proc Biol Sci 272: 2073-2081.
19. Pounder JI, Simmon KE, Barton CA, Hohmann SL, Brandt ME, et al. (2007) Discovering potential pathogens among fungi identified as nonsporulating molds. J Clin Microbiol 45: 568-571.
20. Atkins SD, Clark IM, (2004) Fungal molecular diagnostics: a mini review. J Appl Genet 45 3-15: 178.
21. Dong W, Liu J, Yu J, Wang L, Zhou S, (2012) Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding. PLoS One 7(4): e35071.
22. Taberlet P, Gielly L, Pautou G, Bouvet J, (1991) Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol Biol 17: 1105-1109.
23. Khatib R, Riederer KM, Ramanathan J, Baran J Jr, (2001) Faecal fungal flora in healthy volunteers and inpatients. Mycoses 44: 151-156.
24. Goerges S, Mounier J, Rea MC, Gelsomino R, Heise V, et al. (2008) Commercial ripening starter microorganisms inoculated into cheese milk do not successfully establish themselves in the resident microbial ripening consortia of a South german red smear cheese. Appl Environ Microbiol 74: 2210-2217.
25. Giraud F, Giraud T, Aguileta G, Fournier E, Samson R, et al. (2010) Microsatellite loci to recognize species for the cheese starter and contaminating strains associated with cheese manufacturing. Int J Food Microbiol 137: 204-213.
26. Ghannoum MA, Jurevic RJ, Mukherjee PK, Cui F, Sikaroodi M, et al. (2010) Characterization of the oral fungal microbiome (mycobiome) in healthy individuals. PLoS Pathog 6: e1000713.
27. Asefa DT, Gjerde RO, Sidhu MS, Langsrud S, Kure CF, et al. (2009) Moulds contaminants on Norwegian dry-cured meat products. Int J Food Microbiol 128: 435-439.
28. Rodriguez A, Rodriguez M, Andrade MJ, Cordoba JJ, (2012) Development of a multiplex real-time PCR to quantify aflatoxin, ochratoxin A and patulin producing molds in foods. Int J Food Microbiol 155: 10-18.
29. Klich MA, (2009) Health effects of Aspergillus in food and air. Toxicol Ind Health 25: 657-667.
30. Saleh A Kabli, (2007) Studies on Fungal Communities Associated with Litter of Plant Cover at Al-Taif Province, Saudi Arabia. Met env and Arid Land Agric, Sci 18: 87-98.
31. Valdez JG, Makuch MA, Ordovini AF, Frisvad JC, Overy DP, et al. (2009) Identification, pathogenicity and distribution of Penicillium spp. isolated from garlic in two regions in Argentina. Plant pathology 58: 352-361.
32. Inoue Y, Matsuwaki Y, Shin SH, Ponikau JU, Kita H, (2005) Nonpathogenic, environmental fungi induce activation and degranulation of human eosinophils. J Immunol 175: 5439-5447.
33. Sonjak S, Licen M, Frisvad JC, Gunde-Cimerman N, (2011) The mycobiota of three dry-cured meat products from Slovenia. Food Microbiol 28: 373-376.
34. Bragulat MR, Abarca ML, Cabanes FJ, (2008) Low occurrence of patulin- and citrinin-producing species isolated from grapes. Letters in Applied Microbiology 47: 286-289.
35. Westwood GS, Huang SW, Keyhani NO, (2005) Allergens of the entomopathogenic fungus Beauveria bassiana. Clin Mol Allergy 3: 1.
36. Ann Chai LY, Denning DW, Warn P, (2010) Candida tropicalis in human disease. Crit Rev Microbiol 36: 282-298.
37. Yim SM, Kim JY, Ko JH, Lee YW, Choe YB, et al. (2010) Molecular analysis of Malassezia microflora on the skin of the patients with atopic dermatitis. Ann Dermatol 22: 41-47.
38. Lee YW, Byun HJ, Kim BJ, Kim DH, Lim YY, et al. (2011) Distribution of Malassezia species on the scalp in korean seborrheic dermatitis patients. Ann Dermatol 23: 156-161.
39. Abdullahi I, Koerbler M, Stachewicz H, Winter S, (2005) The 18S rDNA sequence of Synchytrium endobioticum and its utility in microarrays for the simultaneous detection of fungal and viral pathogens of potato. Appl Microbiol Biotechnol 68: 368-375.
40. Pandey PK, Siddharth J, Verma P, Bavdekar A, Patole MS, et al. (2012) Molecular typing of fecal eukaryotic microbiota of human infants and their respective mothers. J Biosci 37: 221-226.
41. Hong MH, Kim JH, Bae H, Lee NY, Shin YC, et al. (2010) Atractylodes japonica inhibits the production of proinflammatory cytokines through inhibition of the NF-kappaB/IkappaB signal pathway in HMC-1 human mast cells. Arch Pharm Res 33: 843-851.
42. Parfrey LW, Walters WA, Knight R, (2011) Microbial eukaryotes in the human microbiome: ecology, evolution, and future directions. Front Microbiol 2: 153.
43. Wright SG, (2012) Protozoan infections of the gastrointestinal tract. Infect Dis Clin North Am 26 (2): 2323-2339.
44. Kullberg BJ, Oude Lashof AM, (2002) Epidemiology of opportunistic invasive mycoses. Eur J Med Res 7(5): 183-191.
45. Kimura M, (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16: 111-120.
46. Leeming JP, Notman FH, (1987) Improved methods for isolation and enumeration of Malassezia furfur from human skin. J Clin Microbiol 25: 2017-2019.
47. Thomas V, Herrera-Rimann K, Blanc DS, Greub G, (2006) Biodiversity of amoebae and amoeba-resisting bacteria in a hospital water network. Appl Environ Microbiol 72: 2428-2438.
48. Schroeder JM, Booton GC, Hay J, Niszl IA, Seal DV, et al. (2001) Use of subgenic 18S ribosomal DNA PCR and sequencing for genus and genotype identification of Acanthamoeba from humans with keratitis and from sewage sludge. J Clin Microbiol 39: 1903-1911.
49. Santos HL, Bandea R, Martins LA, de Macedo HW, Peralta RH, et al. (2010) Differential identification of Entamoeba spp. based on the analysis of 18S rRNA. Parasitol Res 106: 883-888.
50. Kuiper MW, Valster RM, Wullings BA, Boonstra H, Smidt H, et al. (2006) Quantitative detection of the free-living amoeba Hartmannella vermiformis in surface water by using real-time PCR. Appl Environ Microbiol 72: 5750-5756.
51. Pelandakis M, Pernin P, (2002) Use of multiplex PCR and PCR restriction enzyme analysis for detection and exploration of the variability in the free-living Amoeba, Naegleria in the environment. Appl Environ Microbiol 68: 2061-2065.
52. Dopheide A, Lear G, Stott R, Lewis G, (2008) Molecular characterization of ciliate diversity in stream biofilms. Appl Environ Microbiol 74: 1740-1747.
53. Provan J, Murphy S, Maggs CA, (2004) Universal plastid primers for Chlorophyta and Rhodophyta. Eur J Phycol 39: 43-50.
54. Senapin S, Phiwsaiya K, Kiatmetha P, Withyachumnarnkul B, (2010) Development of primers and a procedure for specific identification of the diatom Thalassiosira weissflogii. Aquacult Int 19: 693-704.
55. Lin S, Zhang H, Hou Y, Miranda L, Bhattacharya D, (2006) Development of a dinoflagellate-oriented PCR primer set leads to detection of picoplanktonic dinoflagellates from Long Island Sound. Appl Environ Microbiol 72: 5626-5630.
56. Kolisko M, Silberman JD, Cepicka I, Yubuki N, Takishita K, et al. (2010) A wide diversity of previously undetected free-living relatives of diplomonads isolated from marine/saline habitats. Environ Microbiol 12: 2700-2710.
57. Mullner AN, Angeler DG, Samuel R, Linton EW, Triemer RE, (2001) Phylogenetic analysis of phagotrophic, photomorphic and osmotrophic euglenoids by using the nuclear 18S rDNA sequence. Int J Syst Evol Microbiol 51: 783-791.
58. Desquesnes M, McLaughlin G, Zoungrana A, Davila AM, (2001) Detection and identification of Trypanosoma of African livestock through a single PCR based on internal transcribed spacer 1 of rDNA. Int J Parasitol 31: 610-614.
59. Callahan HA, Litaker RW, Noga EJ, (2002) Molecular taxonomy of the suborder Bodonina (Order Kinetoplastida), including the important fish parasite, Ichthyobodo necator. J Eukaryot Microbiol 49: 119-128.
60. Chabchoub N, Abdelmalek R, Mellouli F, Kanoun F, Thellier M, et al. (2009) Genetic identification of intestinal microsporidia species in immunocompromised patients in Tunisia. Am J Trop Med Hyg 80: 24-27.
61. Hayes DC, Anderson RR, Walker RL, (2003) Identification of Trichomonadid protozoa from the bovine preputial cavity by polymerase chain reaction and restriction fragment length polymorphism typing. J Vet Diagn Invest 15: 390-394.
62. Mirhendi H, Makimura K, Zomorodian K, Yamada T, Sugita T, et al. (2005) A simple PCR-RFLP method for identification and differentiation of 11 Malassezia species. J Microbiol Methods 61: 281-284.
63. White T, Burns T, Lee S, Taylor JW (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylognetics. PCR protocols: a guide and applications. New York: Academic Press, Harcourt Brace Jovanovich. 315-322.
64. Stoeck T, Hayward B, Taylor GT, Varela R, Epstein SS, (2006) A multiple PCR-primer approach to access the microeukaryotic diversity in environmental samples. Protist 157: 31-43.