Open AccessThe currently used commercial DNA ‐extraction methods give different results of clostridial and a ctinobacterial populations derived from human fecal samples
Author(s) -
Maukonen Johanna,
Simões Catarina,
Saarela Maria
Publication year - 2012
Publication title -
fems microbiology ecology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.377
H-Index - 155
eISSN - 1574-6941
pISSN - 0168-6496
DOI - 10.1111/j.1574-6941.2011.01257.x
Subject(s) - biology , bacteroides , dna extraction , microbiology and biotechnology , dna , eubacterium , clostridium , lysis , human feces , feces , fecal coliform , roseburia , extraction (chemistry) , bacteria , polymerase chain reaction , genetics , gene , ecology , chromatography , chemistry , water quality
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 B acteroides spp., whereas after a week's storage at −20 °C, the numbers of B acteroides spp. were 1.6–2.5 log units lower ( P < 0.05). Furthermore, the numbers of predominant bacteria, E ubacterium rectale ( E rec)‐group, C lostridium leptum group, bifidobacteria, and A topobium 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 E rec‐group differed significantly after different DNA ‐extractions; after enzymatic DNA ‐extraction, the most prevalent genera detected were R oseburia (39% of clones) and C oprococcus (10%), whereas after mechanical DNA ‐extraction, the most prevalent genera were B lautia (30%), C oprococcus (13%), and D orea (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 a ctinobacterial populations are highly dependent on the DNA ‐extraction methods applied, the use of different DNA ‐extraction protocols may explain the contradictory results previously obtained.