Rapid lab-on-a-chip profiling of human gut bacteria

Joakim Bjerketorp, Albert Ng Tze Chiang, Klas Hjort, Magnus Rosenquist, Wen Tso Liu, Janet K. Jansson

Research output: Contribution to journalArticlepeer-review

Abstract

The human gut microbiota has a substantial impact on human health. Different factors such as disease, diet and drug use can have significant impacts on the gut microbiota. Therefore, it is of interest to have simple, rapid methods for analysis of the composition of the gut microbiota for clinical diagnostic purposes. Since only a minor fraction of the gastrointestinal bacterial community is presently possible to cultivate, molecular approaches are currently the best suited to investigate its composition. However, most of these molecular approaches require technical expertise and expensive equipment to run and they are not routinely available. Ideally, the analyses should be point-of-care options that can be run on a chip. In this study, an existing lab-on-chip (LOC) system for sizing/quantifying DNA was combined with length heterogeneity PCR (LH-PCR), a PCR-based profiling method targeting bacterial 16S rRNA gene sequences, to develop a fast, straightforward, reproducible, and economical method for profiling bacterial communities. The LOC LH-PCR method was first evaluated using a standardized gut cocktail containing genomic DNA from eight different bacterial species representing different genera of relevance for human health. The method was also tested on DNA that was directly extracted from human faecal samples and it was consistently capable of detecting alterations in the bacterial samples before and after antibiotic treatment. Although the resolution of the method needs improvement, this study represents the first step towards development of a diagnostic LOC for profiling gut bacterial communities.

Original languageEnglish (US)
Pages (from-to)82-90
Number of pages9
JournalJournal of Microbiological Methods
Volume72
Issue number1
DOIs
StatePublished - Jan 2008
Externally publishedYes

Keywords

  • Gut cocktail
  • Human gut microbiota
  • Lab-on-a-chip (LOC)
  • Length heterogeneity PCR (LH-PCR)
  • Microbiome

ASJC Scopus subject areas

  • Microbiology
  • Molecular Biology
  • Microbiology (medical)

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