# US 8,771,940 B2 · Array for detecting microbes > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 8,771,940 B2 - Document ID: US8771940B2 - Status: Granted - Kind: B2 - Application number: 12/474,204 - Filed: 2009-05-28 - Published: 2009-11-26 - Granted: 2014-07-08 - Earliest claimed: 2006-11-30 - Assignees: The Regents of the University of California - Applicants: Gary L. Andersen; Todd D. DeSantis - Inventors: Gary L. Andersen; Todd D. DeSantis - Web page: https://patentgrep.com/patent/US8771940B2 ## CPC - C12Q 1/689: for bacteria - G16B 25/00: ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression - C12Q 1/6837: using probe arrays or probe chips (C12Q1/6874 takes precedence) - C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES - G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY ## 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. ## Claims ### Claim 1 A method comprising: applying a sample comprising nucleic acids derived from a plurality of microorganisms representing a plurality of operational taxonomic units (OTUs) to a system, the system comprising (i) a first probe set comprising a plurality of different first nucleic acid probes, each of which is complementary to a 16S rRNA or rDNA sequence that is present only within a first OTU, (ii) a second probe set comprising a plurality of different second nucleic acid probes, each of which is complementary to a 16S rRNA or rDNA sequence that is present in more than one OTU but collectively are present only in a second OTU, wherein the second OTU is different than the first OTU, and (iii) a third probe set consisting of a plurality of different third nucleic acid probes for detecting a third OTU, wherein the third nucleic acid probes are complementary to 16S rRNA or rDNA sequences collectively present in the third OTU and another OTU, and are selected to minimize the number of putative cross-reactive OTUs, wherein the third OTU is different from the second OTU and the first OTU; and detecting hybridization between the nucleic acids derived from the plurality of microorganisms and the first, second and third probe sets, and identifying the presence and/or the quantity of microorganisms from the first, second and third OTUs based on the hybridization. ### Claim 2 (depends on 1) The method of claim 1, wherein the plurality of microorganisms comprises bacteria or archaea. ### Claim 3 (depends on 1) The method of claim 1, wherein the system further comprises more than one mismatch probe for each of the nucleic acid probes complementary to 16S rRNA or rDNA sequences, wherein each mismatch probe differs from the nucleic acid probe to which it corresponds at one or more nucleotide bases. ### Claim 4 (depends on 1) The method of claim 1, wherein the OTUs identified in presence and/or quantity are the most metabolically active organisms in the sample. ### Claim 5 A method comprising: applying a sample comprising nucleic acids derived from a plurality of microorganisms representing a plurality of operational taxonomic units (OTUs) to a system, the system comprising: (i) a first probe set comprising at least 11 different first nucleic acid probes, each of said first nucleic acid probes being complementary to a 16S rRNA or rDNA sequence present only in a first OTU, (ii) a second probe set comprising at least 11 different second nucleic acid probes, each of said second nucleic acid probes being complementary to a 16S rRNA or rDNA sequence present in a plurality of OTUs but collectively are present only in a second OTU, wherein the second OTU is different than the first OTU, (iii) a third probe set consisting of at least 11 different third nucleic acid probes for detecting a third OTU, wherein the third nucleic acid probes are complementary to 16S rRNA or rDNA sequences collectively present in the third OTU and another OTU, wherein the third OTU is different from the second OTU and the first OTU, wherein the different third nucleic acid probes are selected to minimize the number of putative cross-reactive OTUs; and detecting hybridization between the nucleic acids derived from the plurality of microorganisms and the first, second and third probe sets, and identifying the presence and/or the quantity of microorganisms from the first, second and third OTUs based on the hybridization. ### Claim 6 (depends on 5) The method of claim 5, wherein the identification is made with a level of confidence of about 90% or higher. ### Claim 7 (depends on 6) The method of claim 6, wherein said level of confidence is 95% or higher. ### Claim 8 (depends on 6) The method of claim 6, wherein said level of confidence is 98% or higher. ### Claim 9 (depends on 1, 5) The method of claim 1 or 5, wherein said sample is an environmental sample. ### Claim 10 (depends on 1, 5) The method of claim 1 or 5, wherein said sample is a clinical sample. ### Claim 11 (depends on 10) The method of claim 10, wherein said clinical sample comprises at least one of tissue, skin, bodily fluid, or blood. ### Claim 12 (depends on 10) The method of claim 10, wherein said clinical sample is a lung sample, a gut sample, an ear sample, a nose sample, a throat sample, or a digestive system sample. ### Claim 13 (depends on 1, 5) The method of claim 1 or 5, wherein said plurality of nucleic acid probes are arranged in an array. ### Claim 14 (depends on 1, 5) The method of claim 1 or 5, wherein said system is capable of detecting about 9000 different OTUs. ### Claim 15 (depends on 1, 5) The method of claim 1 or 5, wherein said nucleic acids are selected from the group consisting of: DNA, RNA, DNA from amplified products, and rRNA. ### Claim 16 (depends on 1, 5) The method of claim 1 or 5, wherein all demarcated bacterial and archaeal orders are represented by said nucleic acid probes. ### Claim 17 (depends on 1, 5) The method of claim 1 or 5, wherein, for a majority of OTUs that can be detected by said system, said nucleic acid probes are complementary to 16S rRNA sequences that have only been identified within a single OTU. ### Claim 18 (depends on 1, 5) The method of claim 1 or 5, further comprising quantifying rRNA molecules present in said sample. ### Claim 19 (depends on 1, 5) The method of claim 1 or 5, wherein at least a subset of said first, second or third nucleic acid probes comprise sequences complementary to 16S rRNA or rDNA sequence fragments, wherein only partial gene sequence is known. ### Claim 20 (depends on 1) The method of claim 1 wherein said system comprises from about 2 to about 200 first, second or third nucleic acid probes complementary to 16S rRNA or rDNA sequences for each of said OTUs. ### Claim 21 (depends on 12) The method of claim 12, wherein said clinical sample is a gut sample. ### Claim 22 (depends on 1, 5) The method of claim 1 or 5, wherein each probe is from about 20 to about 30 by long. ### Claim 23 (depends on 1, 5) The method of claim 1 or 5, wherein each of the probes is a 25-mer. ### Claim 24 (depends on 1, 5) The method of claim 1 or 5, wherein said system further comprises a mismatch probe for each of the plurality of probes in the first set of probes, second set of probes and third set of probes, wherein each of the mismatch probes differs from its respective probe at one or more nucleotide bases based. ### Claim 25 (depends on 1, 5) The method of claim 1 or 5, wherein an OTU is considered present in the sample when at least a threshold percentage of a plurality of probe pairs assigned to it are positive. ### Claim 26 (depends on 25) The method of claim 25, wherein the threshold percentage is >92%. ### Claim 27 (depends on 1, 5) The method of claim 1 or 5, wherein an OTU consists of sequences having up to 3% sequence divergence. ### Claim 28 A method comprising: applying a sample comprising nucleic acids derived from a plurality of microorganisms representing a plurality of operational taxonomic units (OTUs) to a system, the system comprising (i) a first probe set comprising a plurality of different first nucleic acid probes, each of which is complementary to a 16S rRNA or rDNA sequence that is present only within a first OTU, (ii) a second probe set comprising a plurality of different second nucleic acid probes, each of which is complementary to a 16S rRNA or rDNA sequence that is present in more than one OTU but collectively are present only in a second OTU, wherein the second OTU is different than the first OTU, and (iii) a third probe set consisting of a plurality of different third nucleic acid probes for detecting a third OTU, wherein the third nucleic acid probes are complementary to 16S rRNA or rDNA sequences collectively present in the second OTU and the third OTU, and are selected to minimize the number of putative cross-reactive OTUs, wherein the third OTU is different from the second OTU and the first OTU; and detecting hybridization between the nucleic acids derived from the plurality of microorganisms and the first, second and third probe sets, and identifying the presence and/or the quantity of microorganisms from the first, second and third OTUs based on the hybridization.