Abstract: Methods for characterizing a population of microbes in a sample are described. The methods include: amplifying microbial polynucleotides obtained from the sample to form a plurality of amplicons and combining the amplicons with a plurality of microbeads, wherein each of the microbeads has a lanthanide spectral signature paired with the sequence of capture polynucleotides immobilized on the microbead. At least some of the capture polynucleotides comprise a sequence substantially complementary to a microbe-identifying sequence in one or more amplicons, such that at least some amplicons are captured onto beads by the capture polynucleotides and the microbe can be identified based on the lanthanide spectral signature of with which the capture polynucleotide is paired. Further described are methods for the identification of pathogens present in a sample by evaluating patterns of hybridization of a capture oligonucleotide to amplicons.