Compositions and methods for metagenome biomarker detection

Abstract

The present invention provides compositions and methods for the multiplex detection of biomarkers in an environmental, non-biological or biological sample. Compositions and methods are provided for simultaneously detecting and identifying multiple pathogens, including viruses, bacteria, fungi, protozoa and helminths, present in a sample.

What is claimed is: 
     
         1 . A method of selecting a set of probes for the detection of one or more target nucleic acid molecules the method comprising:
 generating a metagenome comprising a plurality of nucleic acid molecules; and   selecting nucleic acid probes that specifically target a unique nucleic acid sequence in the metagenome.   
     
     
         2 . The method of  claim 1 , wherein the step of selecting the probes further hybridizing one or more probes to the metagenome; and
 selecting probes that hybridize to one or more target nucleic acid molecules in the metagenome.   
     
     
         3 . The method of  claim 1 , wherein the metagenome comprise sequences and/or genomes from a plurality of organisms or pathogens. 
     
     
         4 . The method of  claim 3 , wherein the plurality of pathogens comprise two or more pathogens selected from the group consisting of viral, bacterial, fungal, helminth, and protozoan pathogens. 
     
     
         5 . The method of  claim 1 , wherein the metagenome is discrete or concatenated. 
     
     
         6 . The method of  claim 1 , wherein one or more steps is performed using a non-transitory computer readable medium containing program instructions executable by a processor. 
     
     
         7 . A metagenome comprising a plurality of nucleic acid molecules, wherein the nucleic acid molecules comprise sequences or genomes from a plurality of organisms. 
     
     
         8 . The metagenome of  claim 7 , wherein the organism is a pathogen. 
     
     
         9 . The metagenome of  claim 8 , wherein the plurality of pathogens comprise two or more pathogens selected from the group consisting of viral, bacterial, fungal, helminth, and protozoan pathogens. 
     
     
         10 . The metagenome of  claim 9 , comprising two or more pathogens. 
     
     
         11 . The metagenome of  claim 10 , comprising about 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 2000, 3000 or more pathogens. 
     
     
         12 . The metagenome of  claim 7 , comprising two or more genomes. 
     
     
         13 . The metagenome of  claim 12 , comprising about 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 2000, 3000 or more genomes. 
     
     
         14 . The metagenome of  claim 7 , wherein the metagenome is discrete or concatenated. 
     
     
         15 . The metagenome of  claim 7 , comprising a spacer sequence between genomes. 
     
     
         16 . A set of probes for the detection of one or more target nucleic acid molecules made by a method comprising:
 generating a metagenome comprising a plurality of nucleic acid molecules; and   selecting nucleic acid probes that specifically target a unique nucleic acid sequence in the metagenome.   
     
     
         17 . The set of probes of  claim 16 , wherein the probes are bound to a solid substrate. 
     
     
         18 . The set of probes of  claim 17 , wherein the solid substrate comprises a panel, biochip, microarray, membrane, bead, or well. 
     
     
         19 . The set of probes of  claim 17 , arranged in an array. 
     
     
         20 . A method of detecting one or more target nucleic acid sequences in a sample, comprising the use of a set of probes, the set of probes made by a method comprising:
 generating a metagenome comprising a plurality of nucleic acid molecules;   selecting nucleic acid probes that specifically target a unique nucleic acid sequence in the metagenome;   the method comprising hybridizing one or more sample nucleic acid molecules to the set of probes, wherein the sample nucleic molecules are labeled with a detectable moiety; and   detecting a signal from the binding of a nucleic acid probe and a sample nucleic acid molecule labeled with the detectable moiety, as compared to a reference.   
     
     
         21 . The method of  claim 20 , wherein the sample nucleic acid molecules comprise DNA and RNA. 
     
     
         22 . The method of  claim 20 , wherein the sample is an environmental or biological sample. 
     
     
         23 . The method of  claim 20 , wherein the sample nucleic acid molecules are from a plurality of organisms or pathogens. 
     
     
         24 . The method of  claim 23 , wherein the plurality of pathogens comprise two or more pathogens selected from the group consisting of viral, bacterial, fungal, helminth, and protozoan pathogens. 
     
     
         25 . The method of  claim 24 , comprising about 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 2000, 3000 or more pathogens.