Bifidobacterial diversity in human feces detected by genus-specific PCR and denaturing gradient gel electrophoresis

Reetta Satokari (Corresponding Author), Elaine Vaughan, Antoon Akkermans, Maria Saarela, Willem de Vos

Research output: Contribution to journalArticleScientificpeer-review

347 Citations (Scopus)

Abstract

We describe the development and validation of a method for the qualitative analysis of complex bifidobacterial communities based on PCR and denaturing gradient gel electrophoresis (DGGE).Bifidobacterium genus-specific primers were used to amplify an approximately 520-bp fragment from the 16S ribosomal DNA (rDNA), and the fragments were separated in a sequence-specific manner in DGGE. PCR products of the same length from different bifidobacterial species showed good separation upon DGGE. DGGE of fecal 16S rDNA amplicons from five adult individuals showed host-specific populations of bifidobacteria that were stable over a period of 4 weeks. Sequencing of fecal amplicons resulted in Bifidobacterium-like sequences, confirming that the profiles indeed represent the bifidobacterial population of feces. Bifidobacterium adolescentis was found to be the most common species in feces of the human adult subjects in this study. The methodological approach revealed intragenomic 16S rDNA heterogeneity in the type strain of B. adolescentis, E-981074. The strain was found to harbor five copies of 16S rDNA, two of which were sequenced. The two 16S rDNA sequences of B. adolescentis E-981074T exhibited microheterogeneity differing in eight positions over almost the total length of the gene.
Original languageEnglish
Pages (from-to)504-513
Number of pages10
JournalApplied and Environmental Microbiology
Volume67
Issue number2
DOIs
Publication statusPublished - 2001
MoE publication typeA1 Journal article-refereed

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Denaturing Gradient Gel Electrophoresis
denaturing gradient gel electrophoresis
Ribosomal DNA
Feces
feces
ribosomal DNA
Bifidobacterium adolescentis
electrokinesis
gel
Bifidobacterium
DNA
Polymerase Chain Reaction
qualitative analysis
Population
harbor
nucleotide sequences
gene
Genes
genes

Cite this

Satokari, Reetta ; Vaughan, Elaine ; Akkermans, Antoon ; Saarela, Maria ; de Vos, Willem. / Bifidobacterial diversity in human feces detected by genus-specific PCR and denaturing gradient gel electrophoresis. In: Applied and Environmental Microbiology. 2001 ; Vol. 67, No. 2. pp. 504-513.
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abstract = "We describe the development and validation of a method for the qualitative analysis of complex bifidobacterial communities based on PCR and denaturing gradient gel electrophoresis (DGGE).Bifidobacterium genus-specific primers were used to amplify an approximately 520-bp fragment from the 16S ribosomal DNA (rDNA), and the fragments were separated in a sequence-specific manner in DGGE. PCR products of the same length from different bifidobacterial species showed good separation upon DGGE. DGGE of fecal 16S rDNA amplicons from five adult individuals showed host-specific populations of bifidobacteria that were stable over a period of 4 weeks. Sequencing of fecal amplicons resulted in Bifidobacterium-like sequences, confirming that the profiles indeed represent the bifidobacterial population of feces. Bifidobacterium adolescentis was found to be the most common species in feces of the human adult subjects in this study. The methodological approach revealed intragenomic 16S rDNA heterogeneity in the type strain of B. adolescentis, E-981074. The strain was found to harbor five copies of 16S rDNA, two of which were sequenced. The two 16S rDNA sequences of B. adolescentis E-981074T exhibited microheterogeneity differing in eight positions over almost the total length of the gene.",
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Bifidobacterial diversity in human feces detected by genus-specific PCR and denaturing gradient gel electrophoresis. / Satokari, Reetta (Corresponding Author); Vaughan, Elaine; Akkermans, Antoon; Saarela, Maria; de Vos, Willem.

In: Applied and Environmental Microbiology, Vol. 67, No. 2, 2001, p. 504-513.

Research output: Contribution to journalArticleScientificpeer-review

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AB - We describe the development and validation of a method for the qualitative analysis of complex bifidobacterial communities based on PCR and denaturing gradient gel electrophoresis (DGGE).Bifidobacterium genus-specific primers were used to amplify an approximately 520-bp fragment from the 16S ribosomal DNA (rDNA), and the fragments were separated in a sequence-specific manner in DGGE. PCR products of the same length from different bifidobacterial species showed good separation upon DGGE. DGGE of fecal 16S rDNA amplicons from five adult individuals showed host-specific populations of bifidobacteria that were stable over a period of 4 weeks. Sequencing of fecal amplicons resulted in Bifidobacterium-like sequences, confirming that the profiles indeed represent the bifidobacterial population of feces. Bifidobacterium adolescentis was found to be the most common species in feces of the human adult subjects in this study. The methodological approach revealed intragenomic 16S rDNA heterogeneity in the type strain of B. adolescentis, E-981074. The strain was found to harbor five copies of 16S rDNA, two of which were sequenced. The two 16S rDNA sequences of B. adolescentis E-981074T exhibited microheterogeneity differing in eight positions over almost the total length of the gene.

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