Array for detecting microbes

Abstract

The present embodiments relate to an array system for detecting and identifying biomolecules and organisms. More specifically, the present embodiments relate to an array system comprising a microarray configured to simultaneously detect a plurality of organisms in a sample at a high confidence level.

What is claimed is: 
     
         1 . An array system comprising:
 (a) a microarray configured to simultaneously detect a plurality of organisms in a sample, wherein the microarray comprises a plurality of probes attached to a surface comprising (i) a first probe set comprising a plurality of different first nucleic acid probes, each of which is complementary to an rRNA or rDNA sequence that is present in more than one operational taxonomic unit (OTU) but collectively are present only in a first OTU; and (ii) a second probe set consisting of different second nucleic acid probes for detecting a second OTU that is different from the first OTU, wherein the second nucleic acid probes are complementary to rRNA or rDNA sequences collectively present in the first OTU and the second OTU; and   (b) a computer system configured to determine the presence of the second OTU based on hybridization signal intensities from the plurality of probes according to computer-readable code, wherein the computer-readable code provides instructions for (i) calculating a first hybridization score for the first OTU based on signal intensities of the first probe set; (ii) calculating a second hybridization score for the second OTU based on signal intensities of the second probe set; and (iii) determining the presence of the second OTU and the absence of the first OTU when the second hybridization score is above a threshold value and the first hybridization score is below the threshold value.   
     
     
         2 . The system of  claim 1 , wherein the OTUs comprise bacteria or archaea. 
     
     
         3 . The system of  claim 1 , wherein the plurality of probes comprise probes for detecting 9000 OTUs. 
     
     
         4 . The system of  claim 1 , wherein the rRNA or rDNA sequence is a 16S rRNA or rDNA sequence. 
     
     
         5 . The system of  claim 1 , wherein the array further comprises a mismatch probe for each of the nucleic acid probes complementary to rRNA or rDNA sequences, wherein each mismatch probe differs from the nucleic acid probe to which it corresponds at one or more nucleotide bases. 
     
     
         6 . The system of  claim 1 , wherein the array further comprises more than one mismatch probe for each of the nucleic acid probes complementary to rRNA or rDNA sequences, wherein each mismatch probe differs from the nucleic acid probe to which it corresponds at one or more nucleotide bases. 
     
     
         7 . The system of  claim 1 , wherein detecting the presence of the second OTU is made with a level of confidence higher than 95%. 
     
     
         8 . The system of  claim 1 , wherein the microarray is configured to simultaneously detect a plurality of organisms in an environmental sample. 
     
     
         9 . The system of  claim 1 , wherein the microarray is configured to simultaneously detect a plurality of organisms in a clinical sample. 
     
     
         10 . The system of  claim 9 , wherein the clinical sample comprises at least one of tissue, skin, bodily fluid, or blood. 
     
     
         11 . The system of  claim 9 , wherein the clinical sample is a lung sample, a gut sample, an ear sample, a nose sample, a throat sample, or a digestive system sample. 
     
     
         12 . The system of  claim 11 , wherein the clinical sample is a gut sample. 
     
     
         13 . The system of  claim 1 , wherein all demarcated bacterial and archaeal orders are represented by the plurality of probes. 
     
     
         14 . The system of  claim 1 , wherein the computer-readable code further provides instructions for quantifying rRNA molecules present in said sample based on the hybridization signal intensities. 
     
     
         15 . The system of  claim 1 , wherein the first probe set or the second probe set comprises between 2 to 200 different nucleic acid probes. 
     
     
         16 . The system of  claim 1 , wherein the first probe set and the second probe set each comprise 11 or more nucleic acid probes. 
     
     
         17 . The system of  claim 5 , wherein the instructions for calculating the first and second hybridization scores comprise instructions for determining a positive fraction representing the fraction of probe pairs assigned to an OTU that are positive, wherein (i) a probe pair consists of a mismatch probe and the nucleic acid probe to which it corresponds, and (ii) a probe pair is scored as positive based on signal intensities of the probes in the probe pair and signal noise of the array. 
     
     
         18 . The system of  claim 17 , wherein the threshold value is a positive fraction of 92%. 
     
     
         19 . The system of  claim 1 , wherein each of the first and second OTUs consists of sequences having up to 3% sequence divergence. 
     
     
         20 . The system of  claim 1 , wherein each probe in the plurality of probes is between 20 to 30 nucleotides in length. 
     
     
         21 . An array system comprising:
 (a) a microarray having a plurality of probes comprising;
 (i) a first probe set comprising a plurality of different first nucleic acid probes present in a first operational taxon unit (OTU), wherein each of the first nucleic acid probes are complementary to a nucleic acid sequence that is present in more than one operational taxon unit (OTU) but collectively are present only in a first OTU; and 
 (ii) a second probe set for detecting a second OTU and consisting of second nucleic acid probes that are complementary to nucleic acid sequences present in the first OTU and the second OTU, wherein the second OTU is different from the first OTU; and 
   (b) a computer system comprising instructions for determining the presence of the second OTU based on hybridization signal intensities from the plurality of probes by:
 (i) calculating a first hybridization score for the first OTU based on signal intensities of the first probe set; 
 (ii) calculating a second hybridization score for the second OTU based on signal intensities of the second probe set; and 
 (iii) determining the presence of the second OTU and the absence of the first OTU when the second hybridization score is above a threshold value and the first hybridization score is below the threshold value.