Quantification of human fecal Bifidobacterium species by use of quantitative real-time PCR analysis targeting the groEL gene

Applied and Environmental Microbiology

Volumn 78, Issue 8, 2012, Pages 2613-2622

  Junick, Jana ^a   Blaut, Michael ^a  

^a Department of Gastrointestinal Microbiology   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BIFIDOBACTERIUM; BIFIDOBACTERIUM ADOLESCENTIS; CELL NUMBER; COPY NUMBER; DNA EXTRACTION; FECAL SAMPLES; HOUSEKEEPING GENE; HUMAN FECAL; INTER-ASSAY VARIABILITY; MOLECULAR MARKER; QUANTIFICATION LIMIT; QUANTITATIVE REAL TIME PCR; REAL-TIME PCR; REAL-TIME PCR ASSAY;

GENES;

POLYMERASE CHAIN REACTION;

CHAPERONIN;

BACTERIUM; CHROMOSOME; FECES; MICROBIAL COMMUNITY; POLYMERASE CHAIN REACTION; QUANTITATIVE ANALYSIS; REAL TIME; SAMPLING; SPECIES DIVERSITY;

ARTICLE; BACTERIAL LOAD; BIFIDOBACTERIUM; CLASSIFICATION; EVALUATION; FECES; GENETICS; HUMAN; ISOLATION AND PURIFICATION; METHODOLOGY; MICROBIOLOGY; REAL TIME POLYMERASE CHAIN REACTION; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY;

BACTERIAL LOAD; BIFIDOBACTERIUM; CHAPERONIN 60; FECES; HUMANS; REAL-TIME POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY;

BIFIDOBACTERIUM; BIFIDOBACTERIUM ADOLESCENTIS; BIFIDOBACTERIUM ANGULATUM; BIFIDOBACTERIUM ANIMALIS; BIFIDOBACTERIUM BIFIDUM; BIFIDOBACTERIUM BREVE; BIFIDOBACTERIUM CATENULATUM; BIFIDOBACTERIUM DENTIUM; BIFIDOBACTERIUM GALLICUM; BIFIDOBACTERIUM LONGUM; BIFIDOBACTERIUM PSEUDOCATENULATUM; BIFIDOBACTERIUM PSEUDOLONGUM; BIFIDOBACTERIUM THERMOPHILUM; EUKARYOTA;

EID: 84861125910     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.07749-11     Document Type: Article

References (56)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
2. Apajalahti JH, Kettunen A, Nurminen PH, Jatila H, Holben WE. 2003. Selective plating underestimates abundance and shows differential recovery of bifidobacterial species from human feces. Appl. Environ. Microbiol. 69:5731-5735.
3. Bartosch S, Woodmansey EJ, Paterson JC, McMurdo ME, Macfarlane GT. 2005. Microbiological effects of consuming a synbiotic containing Bifidobacterium bifidum, Bifidobacterium lactis, and oligofructose in elderly persons, determined by real-time polymerase chain reaction and counting of viable bacteria. Clin. Infect. Dis. 40:28-37.
4. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. 2011. GenBank. Nucleic Acids Res. 39:D32-D37.
5. Berthoud H, Chavagnat F, Haueter M, Casey MG. 2005. Comparison of partial gene sequences encoding a phosphoketolase for the identification of bifidobacteria. Lebensm. Wiss. Technol. 38:101-105.
6. Biasucci G, Benenati B, Morelli L, Bessi E, Boehm G. 2008. Cesarean delivery may affect the early biodiversity of intestinal bacteria. J. Nutr. 138:1796S-1800S.
7. Biavati B, Mattarelli P. 2006. The family Bifidobacteriaceae, p 322-382. In Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (ed), The prokaryotes, 3rd ed, vol 3. Springer, New York, NY.
8. Bourget N, Simonet JM, Decaris B. 1993. Analysis of the genome of the five Bifidobacterium breve strains: plasmid content, pulsed-field gel electrophoresis genome size estimation and rrn loci number. FEMS Microbiol. Lett. 110:11-20.
9. Braune A, Gütschow M, Engst W, Blaut M. 2001. Degradation of quercetin and luteolin by Eubacterium ramulus. Appl. Environ. Microbiol. 67:5558-5567.
10. Candela M, Vitali B, Matteuzzi D, Brigidi P. 2004. Evaluation of the rrn operon copy number in Bifidobacterium using real-time PCR. Lett. Appl. Microbiol. 38:229-232.
11. Edwards CA, Parrett AM. 2002. Intestinal flora during the first months of life: new perspectives. Br. J. Nutr. 88(Suppl. 1):S11-S18.
12. Fox GE, et al. 1980. The phylogeny of prokaryotes. Science 209:457-463.
13. Fukuda S, et al. 2011. Bifidobacteria can protect from enteropathogenic infection through production of acetate. Nature 469:543-547.
14. Garrigues C, Johansen E, Pedersen MB. 2010. Complete genome sequence of Bifidobacterium animalis subsp. lactis BB-12, a widely consumed probiotic strain. J. Bacteriol. 192:2467-2468.
15. Gavini F, Cayuela C, Antoine JM, Lecoq CLB, Membré JM, Neut C. 2001. Differences in the distribution of bifidobacterial and enterobacterial species in human faecal microflora of three different (children, adults, elderly) age groups. Microb. Ecol. Health Dis. 13:40-45
16. Haarman M, Knol J. 2005. Quantitative real-time PCR assays to identify and quantify fecal Bifidobacterium species in infants receiving a prebiotic infant formula. Appl. Environ. Microbiol. 71:2318-2324
17. Harmsen HJ, et al. 2000. Analysis of intestinal flora development in breast-fed and formula-fed infants by using molecular identification and detection methods. J. Pediatr. Gastroenterol. Nutr. 30:61-67.
18. Hill JE, Penny SL, Crowell KG, Goh SH, Hemmingsen SM. 2004. cpnDB: a chaperonin sequence database. Genome Res. 14:1669-1675.
19. Hopkins MJ, Sharp R, Macfarlane GT. 2001. Age and disease related changes in intestinal bacterial populations assessed by cell culture, 16S rRNA abundance, and community cellular fatty acid profiles. Gut 48:198-205
20. Howie PW, Forsyth JS, Ogston SA, Clark A, Florey CD. 1990. Protective effect of breast feeding against infection. Br. Med. J. 300:11-16.
21. Jian W, Zhu L, Dong X. 2001. New approach to phylogenetic analysis of the genus Bifidobacterium based on partial HSP60 gene sequences. Int. J. Syst. Evol. Microbiol. 51:1633-1638.
22. Kim MS, Roh SW, Bae JW. 2010. Bifidobacterium stercoris sp. nov., isolated from human faeces. Int. J. Syst. Evol. Microbiol. 60:2823-2827.
23. Kullen MJ, Brady LJ, O'Sullivan DJ. 1997. Evaluation of using a short region of the recA gene for rapid and sensitive speciation of dominant bifidobacteria in the human large intestine. FEMS Microbiol. Lett. 154: 377-383.
24. Larkin MA, et al. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23:2947-2948.
25. Leblond-Bourget N, Philippe H, Mangin I, Decaris B. 1996. 16S rRNA and 16S to 23S internal transcribed spacer sequence analyses reveal interand intraspecific Bifidobacterium phylogeny. Int. J. Syst. Bacteriol. 46:102-
26. Mackie RI, Sghir A, Gaskins HR. 1999. Developmental microbial ecology of the neonatal gastrointestinal tract. Am. J. Clin. Nutr. 69:1035S-1045S.
27. Masco L, Ventura M, Zink R, Huys G, Swings J. 2004. Polyphasic taxonomic analysis of Bifidobacterium animalis and Bifidobacterium lactis reveals relatedness at the subspecies level: reclassification of Bifidobacterium animalis as Bifidobacterium animalis subsp. animalis subsp. nov. and Bifidobacterium lactis as Bifidobacterium animalis subsp. lactis subsp. nov. Int. J. Syst. Evol. Microbiol. 54:1137-1143.
28. Mathys S, Lacroix C, Mini R, Meile L. 2008. PCR and real-time PCR primers developed for detection and identification of Bifidobacterium thermophilum in faeces. BMC Microbiol. 8:179.
29. Matsuki T, et al. 2004. Quantitative PCR with 16S rRNA-gene-targeted species-specific primers for analysis of human intestinal bifidobacteria. Appl. Environ. Microbiol. 70:167-173.
30. Matsuki T, Watanabe K, Tanaka R, Fukuda M, Oyaizu H. 1999. Distribution of bifidobacterial species in human intestinal microflora examined with 16S rRNA-gene-targeted species-specific primers. Appl. Environ. Microbiol. 65:4506-4512.
31. Miyake T, Watanabe K, Watanabe T, Oyaizu H. 1998. Phylogenetic analysis of the genus Bifidobacterium and related genera based on 16S rDNA sequences. Microbiol. Immunol. 42:661-667.
32. Morita H, et al. 2011. Bifidobacterium kashiwanohense sp. nov., isolated from healthy infant faeces. Int. J. Syst. Evol. Microbiol. 61:2610-2615.
33. Mullié C, Odou MF, Singer E, Romond MB, Izard D. 2003. Multiplex PCR using 16S rRNA gene-targeted primers for the identification of bifidobacteria from human origin. FEMS Microbiol. Lett. 222:129-136.
34. Nadkarni MA, Martin FE, Jacques NA, Hunter N. 2002. Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set. Microbiology 148:257-266.
35. Owczarzy R, et al. 2008. IDT SciTools: a suite for analysis and design of nucleic acid oligomers. Nucleic Acids Res. 36:W163-W169.
36. Pfaffl MW. 2001. Development and validation of an externally standardised quantitative insulin-like growth factor-1 RT-PCR using LightCycler SYBR Green I technology, p 281-292. In Meuer S, Wittwer C, Nakagawara K (ed), Rapid cycle real-time PCR: methods and applications. Springer, Heidelberg, Germany.
37. Requena T, et al. 2002. Identification, detection, and enumeration of human Bifidobacterium species by PCR targeting the transaldolase gene. Appl. Environ. Microbiol. 68:2420-2427.
38. Reuter G. 2001. The Lactobacillus and Bifidobacterium microflora of the human intestine: composition and succession. Curr. Issues Intest. Microbiol. 2:43-53.
39. Rinne MM, et al. 2005. Similar bifidogenic effects of prebioticsupplemented partially hydrolyzed infant formula and breastfeeding on infant gut microbiota. FEMS Immunol. Med. Microbiol. 43:59-65.
40. Satokari RM, Vaughan EE, Akkermans AD, Saarela M, de Vos WM. Bifidobacterial diversity in human feces detected by genus-specific PCR and denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 67:504-513.
41. Satokari RM, et al. 2003. Molecular approaches for the detection and identification of bifidobacteria and lactobacilli in the human gastrointestinal tract. Syst. Appl. Microbiol. 26:572-584.
42. Schell MA, et al. 2002. The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proc. Natl. Acad. Sci. U. S. A. 99:14422-14427.
43. Turroni F, et al. 2010. Genome analysis of Bifidobacterium bifidum PRL2010 reveals metabolic pathways for host-derived glycan foraging. Proc. Natl. Acad. Sci. U. S. A. 107:19514-19519.
44. Turroni F, et al. 2009. Exploring the diversity of the bifidobacterial population in the human intestinal tract. Appl. Environ. Microbiol. 75:1534-
45. Turroni F, et al. 2009. Microbiomic analysis of the bifidobacterial population in the human distal gut. ISME J. 3:745-751.
46. van Odijk J, et al. 2003. Breastfeeding and allergic disease: a multidisciplinary review of the literature (1966-2001) on the mode of early feeding in infancy and its impact on later atopic manifestations. Allergy 58:833-
47. Ventura M, et al. 2006. Analysis of bifidobacterial evolution using a multilocus approach. Int. J. Syst. Evol. Microbiol. 56:2783-2792.
48. Ventura M, Canchaya C, Meylan V, Klaenhammer TR, Zink R. 2003. Analysis, characterization, and loci of the tuf genes in Lactobacillus and Bifidobacterium species and their direct application for species identification. Appl. Environ. Microbiol. 69:6908-6922.
49. Ventura, M, Canchaya C, van Sinderen D, Fitzgerald GF, Zink R. 2004. Bifidobacterium lactis DSM 10140: identification of the atp (atpBEFHAGDC) operon and analysis of its genetic structure, characteristics, and phylogeny. Appl. Environ. Microbiol. 70:3110-3121.
50. Ventura M, Canchaya C, Zink R, Fitzgerald GF, van Sinderen D. 2004. Characterization of the groEL and groES loci in Bifidobacterium breveUCC [2003:] genetic, transcriptional, and phylogenetic analyses. Appl. Environ. Microbiol. 70:6197-6209
51. Ventura M, Zink R. 2003. Comparative sequence analysis of the tuf and recA genes and restriction fragment length polymorphism of the internal transcribed spacer region sequences supply additional tools for discriminating Bifidobacterium lactis from Bifidobacterium animalis. Appl. Environ. Microbiol. 69:7517-7522.
52. Ventura M, Zink R, Fitzgerald GF, van Sinderen D. 2005. Gene structure and transcriptional organization of the dnaK operon of Bifidobacterium breve UCC 2003 and application of the operon in bifidobacterial tracing. Appl. Environ. Microbiol. 71:487-500.
53. von Ah U, et al. 2007. Classification of a moderately oxygen-tolerant isolate from baby faeces as Bifidobacterium thermophilum. BMC Microbiol. 7:79.
54. Yin X, Chambers JR, Barlow K, Park AS, Wheatcroft R. 2005. The gene encoding xylulose-5-phosphate/fructose-6-phosphate phosphoketolase (xfp) is conserved among Bifidobacterium species within a more variable region of the genome and both are useful for strain identification. FEMS Microbiol. Lett. 246:251-257.
55. Zhu L, Li W, Dong X. 2003. Species identification of genus Bifidobacterium based on partial HSP60 gene sequences and proposal of Bifidobacterium thermacidophilum subsp. porcinum subsp. nov. Int. J. Syst. Evol. Microbiol. 53:1619-1623.
56. Zhurina D, et al. 2011. Complete genome sequence of Bifidobacterium bifidum S17. J. Bacteriol. 193:301-302.