The currently used commercial DNA-extraction methods give different results of clostridial and actinobacterial populations derived from human fecal samples

Johanna Maukonen (Corresponding Author), Catarina Simões, Maria Saarela

Research output: Contribution to journalArticleScientificpeer-review

69 Citations (Scopus)

Abstract

Recently several human health-related microbiota studies have had partly contradictory results. As some differences may be explained by methodologies applied, we evaluated how different storage conditions and commonly used DNA-extraction kits affect bacterial composition, diversity, and numbers of human fecal microbiota. According to our results, the DNA-extraction did not affect the diversity, composition, or quantity of Bacteroides spp., whereas after a week's storage at −20 °C, the numbers of Bacteroides spp. were 1.6–2.5 log units lower (P < 0.05). Furthermore, the numbers of predominant bacteria, Eubacterium rectale (Erec)-group, Clostridium leptum group, bifidobacteria, and Atopobium group were 0.5–4 log units higher (P < 0.05) after mechanical DNA-extraction as detected with qPCR, regardless of storage. Furthermore, the bacterial composition of Erec-group differed significantly after different DNA-extractions; after enzymatic DNA-extraction, the most prevalent genera detected were Roseburia (39% of clones) and Coprococcus (10%), whereas after mechanical DNA-extraction, the most prevalent genera were Blautia (30%), Coprococcus (13%), and Dorea (10%). According to our results, rigorous mechanical lysis enables detection of higher bacterial numbers and diversity from human fecal samples. As it was shown that the results of clostridial and actinobacterial populations are highly dependent on the DNA-extraction methods applied, the use of different DNA-extraction protocols may explain the contradictory results previously obtained.
Original languageEnglish
Pages (from-to)697-708
Number of pages12
JournalFEMS Microbiology Ecology
Volume79
Issue number3
DOIs
Publication statusPublished - 2012
MoE publication typeA1 Journal article-refereed

Fingerprint

extraction method
DNA
Population
Eubacterium
Bacteroides
Microbiota
Bifidobacterium
Clostridium
lysis
clone
Clone Cells
Bacteria
bacterium
methodology
Health

Keywords

  • gut microbiota
  • Actinobacteria
  • DNA-extraction
  • storage

Cite this

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title = "The currently used commercial DNA-extraction methods give different results of clostridial and actinobacterial populations derived from human fecal samples",
abstract = "Recently several human health-related microbiota studies have had partly contradictory results. As some differences may be explained by methodologies applied, we evaluated how different storage conditions and commonly used DNA-extraction kits affect bacterial composition, diversity, and numbers of human fecal microbiota. According to our results, the DNA-extraction did not affect the diversity, composition, or quantity of Bacteroides spp., whereas after a week's storage at −20 °C, the numbers of Bacteroides spp. were 1.6–2.5 log units lower (P < 0.05). Furthermore, the numbers of predominant bacteria, Eubacterium rectale (Erec)-group, Clostridium leptum group, bifidobacteria, and Atopobium group were 0.5–4 log units higher (P < 0.05) after mechanical DNA-extraction as detected with qPCR, regardless of storage. Furthermore, the bacterial composition of Erec-group differed significantly after different DNA-extractions; after enzymatic DNA-extraction, the most prevalent genera detected were Roseburia (39{\%} of clones) and Coprococcus (10{\%}), whereas after mechanical DNA-extraction, the most prevalent genera were Blautia (30{\%}), Coprococcus (13{\%}), and Dorea (10{\%}). According to our results, rigorous mechanical lysis enables detection of higher bacterial numbers and diversity from human fecal samples. As it was shown that the results of clostridial and actinobacterial populations are highly dependent on the DNA-extraction methods applied, the use of different DNA-extraction protocols may explain the contradictory results previously obtained.",
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author = "Johanna Maukonen and Catarina Sim{\~o}es and Maria Saarela",
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The currently used commercial DNA-extraction methods give different results of clostridial and actinobacterial populations derived from human fecal samples. / Maukonen, Johanna (Corresponding Author); Simões, Catarina; Saarela, Maria.

In: FEMS Microbiology Ecology, Vol. 79, No. 3, 2012, p. 697-708.

Research output: Contribution to journalArticleScientificpeer-review

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T1 - The currently used commercial DNA-extraction methods give different results of clostridial and actinobacterial populations derived from human fecal samples

AU - Maukonen, Johanna

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