Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving nucleic acid
Patent
1998-08-13
2000-08-22
Horlick, Kenneth R.
Chemistry: molecular biology and microbiology
Measuring or testing process involving enzymes or...
Involving nucleic acid
435 5, 435 81, 436501, 536 231, 536 241, 536 243, 536 2431, 536 2432, 536 2433, 935 77, 935 78, C12Q 168
Patent
active
061070335
DESCRIPTION:
BRIEF SUMMARY
The invention relates to methods and materials for determining the relative abundance of individual microorganisms in mixed populations of microorganisms, in particular to such methods for determining relative abundance of individual microorganism species in the indigenous gut flora, especially of humans.
Such methods have not been available until the present invention. What has been possible until the present invention is determination of the presence of individual microorganism species in a mixed population such as the intestinal flora.
Traditional methods to determine the composition of the intestinal flora require culturing of the microorganisms in the population on both selective and non-selective media. These methods are laborious and time consuming, which in itself makes it hardly possible to do anything beyond identifying the microorganisms present in the mixed population. Furthermore these methods are prone to methodological and statistical error. Another barrier for determination of abundance of one microorganism via a vis others (relative abundance) is that culturing includes multiplication of the microorganisms which of course do not divide at the same rate. Therefore determination of relative abundance is practically not possible using these methods, let alone that the dynamics of such a population through time could be followed.
The composition and activity of the indigenous gut flora is of paramount importance to human immunology, nutrition, pathogenesis and hence to health of individuals (Van der Waaij et al., 1971). Colonization resistance, or bacterial antagonism of the indigenous intestinal microflora for instance represents a first line of defence against the establishment of pathogenic microorganisms in the intestinal tract (Van der Waaij et al., 1971; 1989).
The human (mammalian) intestinal tract is not the only mixed population of microorganisms for which measuring the relative abundance of individual species or other subgroups of microorganisms is useful or important.
In industry, specifically in the food sector and fermentation industry, monitoring of the bacteria- or yeast-dependent fermentation process is essential for quality assurance both with respect to hygiene and product stability. Environmentally, monitoring of complex mixed bacterial populations is elemental in predicting the effectiveness of bioremediation in soil-, gas- and waste water-treatment. Environmental microbiologists are in need for tools that explain nutrient regeneration potentials in terms of biomass of individual metabolic clusters of bacteria.
Although much is known of the physiology of most bacterial species individually and of metabolic activities of mixed bacterial consortia as a whole, factors that determine their abundance and those causing subtle as well as dramatic changes in population composition have remained largely unknown due to the technical limitations of the classical cultivation and identification techniques. Therefore, rapid monitoring techniques that can unravel the population compositions of complex mixed bacterial consortia are of great scientific importance.
The invention thus provides a rapid and reliable method for determining the relative abundance of individual species or lower phylogenetic groups of microorganisms in a mixed population of several microorganisms comprising the steps of: oligonucleotide probes;
In situ hybridization in itself is a well known technique, as can be read from EP-A-0 497 464, which relates to in situ hybridization techniques using fixed, permeabilized but not mounted cells. The method is used to determine the presence of single microorganisms. So far in situ hybridizaton has however not been applied to determine the relative abundance of lower phylogenetic subclasses, let alone following the dynamics of a mixed population of microorganisms. Labelled probes are an essential part in in situ hybridization. The present invention provides a set of cluster probes which have been chosen in an unexpected novel manner, i.e. not based on the normal taxonomic prin
REFERENCES:
patent: 5679520 (1997-10-01), Hogan et al.
Giovannoni et al. Phylogenetic Group-Specific Oligodeoxynucleotide Probes . . . Journal of Bacteriology. Feb. 1988, vol. 170, No. 2. p. 720-726.
Elffrich Peter
Jansen Gijsbert Johan
Langendijk Petra Simone
Schut Frederik
Welling Gjalt Wietze
Fink Edward M.
Horlick Kenneth R.
Michaelson Peter L.
Microscreen B.V.
Rijksuniversiteit Groningen
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