Gene chip for bacterial indentification?

Question

Can anyone outline the brief steps in which one can make a microarray to identify bacteria. I know we need to use 16SrRNA gene but I want to know what probes will be present on the microarray and how we can proceed

Answer 1

In a bioterrorism event, a tool is needed to rapidly differentiate Bacillus anthracis from other closely related spore-forming Bacillus species. During the recent outbreak of bioterrorism-associated anthrax, we sequenced the 16S rRNA generom these species to evaluate the potential of 16S rRNA gene sequencing as a diagnostic tool. We found eight distinct 16S types among all 107 16S rRNA gene seqs fuences that differed from each other at 1 to 8 positions (0.06% to 0.5%). All 86 B. anthracis had an identical 16S gene sequence, designated type 6; 16S type 10 was seen in all B. thuringiensis strains; six other 16S types were found among the 10 B. cereus strains. This report describes the first demonstration of an exclusive association of a distinct 16S sequence with B. anthracis. Consequently, we were able to rapidly identify suspected isolates and to detect the B. anthracis 16S rRNA gene directly from culture-negative clinical specimens from seven patients with laboratory-confirmed anthrax.

The gram-positive, rod-shaped, and spore-forming bacterium Bacillus anthracis is the cause of the acute and often lethal disease anthrax. Phenotypic characteristics commonly used to differentiate B. anthracis from closely related B. cereus and B. thuringiensis, such as susceptibility to b-lactam antibiotics, lack of motility, lack of hemolysis on sheep blood agar (SBA) plate, and susceptibility to g-phage lysis, may vary among different Bacillus species strains, hampering their identification and differentiation. Phenotypically and genotypically B. thuringiensis can be differentiated from B. cereus by the presence of the CRY crystal protein and plasmid-encoded cry genes (1), but if this plasmid were lost, B. thuringiensis could no longer be distinguished from B. cereus (1). The sequence of the 16S rRNA gene has been widely used as a molecular clock to estimate relationships among bacteria (phylogeny), but more recently it has also become important as a means to identify an unknown bacterium to the genus or species level. The 16S rRNA gene sequences of B. anthracis, B. cereus, and B. thuringiensis have high levels of sequence similarity (>99%) that support their close relationships shown by DNA hybridization (2–7). A limited number of 16S rRNA sequences of B. anthracis (7 sequences), B. cereus (34 sequences), and B. thuringiensis (16 sequences) have been available at GenBank. Although those sequences are of different lengths and qualities, in complementary regions they differ from each other by no more than a few nucleotides. Therefore, this minimal level of diversity seen in the 16S rRNA of B. anthracis, B. cereus, and B. thuringiensis was thought to be an obstacle for using 16S rRNA gene sequencing to identify and differentiate these three species. The bioterrorism events of October 2001 prompted us to evaluate several new molecular approaches to rapidly identify B. anthracis. We determined the entire 16S rRNA sequences in a large number of representative strains of B. anthracis, B. cereus, and B. thuringiensis to evaluate the potential of 16S rRNA sequencing not only to rapidly identify B. anthracis in culture, but also to detect B. anthracis directly in clinical specimens.