Scientist - News - 04-02-2009:
«BackHigh-throughput analysis unravels secrets of GI tract microbiota Beintema, Nienke A review article in Gut describes recent developments in analyzing the vast diversity of microbiota that inhabit our gastrointestinal (GI) tract. The authors argue that high-throughput technologies are indispensable to further identify GI micro-organisms and their role in health and disease. Trillions of bacteria inhabit the human gut. It is estimated that they outnumber our human body cells by a factor of ten. The majority of these microbes are yet unknown. An estimated 50 to 90% of them cannot be cultured by microbiological techniques. This makes it difficult to identify them, let alone to formulate hypotheses about their role in health and disease. Researchers around the world are therefore searching for techniques to identify and study GI microbes without having to culture them in a lab. The Laboratory of Microbiology at Wageningen University, led by Spinoza Prize laureate Willem de Vos, is operating on the forefront of these developments. This research group published a review article on the latest technologies in the November issue of the journal Gut. The review also includes their own research that is being carried out within various EU projects and the Top Institute Food and Nutrition. Since the introduction of culture-independent technologies over a decade ago, explains Erwin Zoetendal, lead author of the Gut paper, the composition of GI tract bacteria has been extensively described on the basis of the nucleotide sequences of 16S ribosomal RNA, or rRNA. "rRNA is part of the ribosomes, or ‘protein factories’, of living cells," he says, "and both the structure and function of this rRNA are comparable between different organisms. Moreover, genes encoding rRNA have a low mutation rate. Differences in rRNA between life forms therefore represent the ‘evolutionary distance’ between them. Organisms can usually be classified at the species level based on their rRNA sequences." New hypotheses Research in the past decade has identified various relationships between the diversity and composition of the GI microbiota and human health. Patients with inflammatory bowel disease (IBD), for instance, have a different microbiota compared to healthy people. However, large differences exist between individuals. "Since the microbiota of a single individual may consist of up to 1,000 different species, novel ‘high-throughput’ technologies are indispensable to make a detailed analysis of much larger numbers of samples," says Zoetendal. "Such analysis, in turn, makes it much easier to find statistically relevant correlations, for instance between certain diseases and certain bacterial groups." The Wageningen laboratory primarily uses the so-called Human Intestinal Tract Chip (HITChip). These diagnostic micro-arrays consist of thousands of rRNA probes, which target all currently known GI tract bacteria, attached to a small chip. These fragments are hybridized with rRNA fragments derived from the sample in question. Fluorescence techniques make it possible to visualize which rRNA fragments hybridized, and thus were present in the sample. Zoetendal: "This technique allows for quantitative as well as qualitative analysis." The micro-array technology is fast: within a week, several dozens of samples can be analyzed to the genus level. "This is impossible with classical rRNA-based technologies," states Zoetendal. "The new technology makes it much easier to identify additional relationships between diseases and bacterial groups, and to formulate new, specific hypotheses." More information: Review article by Zoetendal et. al. (2008) in the journal Gut Wageningen Laboratory of Microbiology |