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Open Access Highly Accessed Methodology article

A short-oligonucleotide microarray that allows improved detection of gastrointestinal tract microbial communities

Carl R Harrington1*, Sacha Lucchini2, Karyn P Ridgway1, Udo Wegmann1, Tracy J Eaton1, Jay CD Hinton2, Michael J Gasson1 and Arjan Narbad1

Author affiliations

1 Commensals and Microflora, Institute of Food Research, Norwich Research Park, Colney Lane, Norwich, Norfolk, NR4 7UA, UK

2 Pathogens: Molecular Microbiology, Institute of Food Research, Norwich Research Park, Colney Lane, Norwich, Norfolk, NR4 7UA, UK

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Citation and License

BMC Microbiology 2008, 8:195  doi:10.1186/1471-2180-8-195

Published: 11 November 2008

Abstract

Background

The human gastrointestinal (GI) tract contains a diverse collection of bacteria, most of which are unculturable by conventional microbiological methods. Increasingly molecular profiling techniques are being employed to examine this complex microbial community. The purpose of this study was to develop a microarray technique based on 16S ribosomal gene sequences for rapidly monitoring the microbial population of the GI tract.

Results

We have developed a culture-independent, semi-quantitative, rapid method for detection of gut bacterial populations based on 16S rDNA probes using a DNA microarray. We compared the performance of microarrays based on long (40- and 50-mer) and short (16–21-mer) oligonucleotides. Short oligonucleotides consistently gave higher specificity. Optimal DNA amplification and labelling, hybridisation and washing conditions were determined using a probe with an increasing number of nucleotide mismatches, identifying the minimum number of nucleotides needed to distinguish between perfect and mismatch probes. An independent PCR-based control was used to normalise different hybridisation results, and to make comparisons between different samples, greatly improving the detection of changes in the gut bacterial population. The sensitivity of the microarray was determined to be 8.8 × 104 bacterial cells g-1 faecal sample, which is more sensitive than a number of existing profiling methods. The short oligonucleotide microarray was used to compare the faecal flora from healthy individuals and a patient suffering from Ulcerative Colitis (UC) during the active and remission states. Differences were identified in the bacterial profiles between healthy individuals and a UC patient. These variations were verified by Denaturing Gradient Gel Electrophoresis (DGGE) and DNA sequencing.

Conclusion

In this study we demonstrate the design, testing and application of a highly sensitive, short oligonucleotide community microarray. Our approach allows the rapid discrimination of bacteria inhabiting the human GI tract, at taxonomic levels ranging from species to the superkingdom bacteria. The optimised protocol is available at: http://www.ifr.ac.uk/safety/microarrays/#protocols webcite. It offers a high throughput method for studying the dynamics of the bacterial population over time and between individuals.