Bead-beating artefacts in the Bacteroidetes to Firmicutes ratio of the human stool metagenome

Heidi C Vebø; Magdalena Kauczynska Karlsson; Ekaterina Avershina; Lene Finnby; Knut Rudi

doi:10.1016/j.mimet.2016.08.005

Bead-beating artefacts in the Bacteroidetes to Firmicutes ratio of the human stool metagenome

J Microbiol Methods. 2016 Oct:129:78-80. doi: 10.1016/j.mimet.2016.08.005. Epub 2016 Aug 4.

Authors

Heidi C Vebø¹, Magdalena Kauczynska Karlsson¹, Ekaterina Avershina², Lene Finnby¹, Knut Rudi³

Affiliations

¹ Genetic Analysis AS, Oslo, Norway.
² Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
³ Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway. Electronic address: knut.rudi@nmbu.no.

PMID: 27498349
DOI: 10.1016/j.mimet.2016.08.005

Abstract

We evaluated bead-beating cell-lysis in analysing the human stool metagenome, since this is a key step. We observed that two different bead-beating instruments from the same producer gave a three-fold difference in the Bacteroidetes to Firmicutes ratio. This illustrates that bead-beating can have a major impact on downstream metagenome analyses.

Keywords: Bead-beating; Human; Metagenome.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Artifacts
Bacteroidetes / genetics*
Bacteroidetes / isolation & purification
DNA, Bacterial / genetics
Feces / microbiology*
Firmicutes / genetics*
Firmicutes / isolation & purification
Humans
Metagenome*
Microspheres
Phylogeny
Real-Time Polymerase Chain Reaction* / methods
Specimen Handling* / methods

Substances

DNA, Bacterial