A method of taxonomically classifying organisms in a heterogeneous microbial sample comprising: providing a heterogeneous microbial sample from an animal subject comprising microbial RNA and host RNA; obtaining ribonucleic acids comprising a metagenomic transcriptome from which microbial rRNA and host rRNA have been removed from the heterogeneous microbial sample; reverse transcribing the ribonucleic acids from the heterogeneous microbial sample into cDNA; obtaining, in electronic form, metatranscriptomic sequence information representative of the ribonucleic acids by high throughput sequencing of the cDNA, the metatranscriptomic sequence information comprising a plurality of nucleotide sequences; assaying, at a computer comprising at least one processor and a memory storing at least one program for execution by the at least one processor, for a presence of a sequence signature in the heterogeneous microbial sample informative of each of a plurality of microbial taxa by mapping all of the nucleotide sequences to a metagenomic library of taxonomic signatures comprising nucleotide sequences specific for microorganisms and a host genome, wherein: the metagenomic library of taxonomic signatures comprises, for each respective microbial taxon in the plurality of microbial taxa, a distinct set of k-mers determined from genomes of the microbial taxa, for each respective microbial taxon in the plurality of microbial taxa, the distinct set of k-mers is formed by removing k-mers that are present in more than one microbial taxa in the plurality of microbial taxa, based on a comparison across different microbial taxa, the plurality of microbial taxa are of the same taxonomic rank, each respective taxonomic signature in the metagenomic library of taxonomic signatures is at least 20 nucleotides long, and k is an integer between 5 and 100; assaying for a presence of each of a plurality of biochemical activities in the heterogeneous microbial sample by mapping the nucleotide sequences to a nucleic acid library comprising open reading frames and identifying genes associated with the biochemical activities encoded by the open reading frame; and using a presence of a sequence signature for one or more microbial taxa in the plurality of microbial taxa to characterize a microbial composition of the heterogenous microbial sample. providing a heterogeneous microbial sample from an animal subject comprising microbial RNA and host RNA; obtaining ribonucleic acids comprising a metagenomic transcriptome from which microbial rRNA and host rRNA have been removed from the heterogeneous microbial sample; reverse transcribing the ribonucleic acids from the heterogeneous microbial sample into cDNA; obtaining, in electronic form, metatranscriptomic sequence information representative of the ribonucleic acids by high throughput sequencing of the cDNA, the metatranscriptomic sequence information comprising a plurality of nucleotide sequences; assaying, at a computer comprising at least one processor and a memory storing at least one program for execution by the at least one processor, for a presence of a sequence signature in the heterogeneous microbial sample informative of each of a plurality of microbial taxa by mapping all of the nucleotide sequences to a metagenomic library of taxonomic signatures comprising nucleotide sequences specific for microorganisms and a host genome, wherein: the metagenomic library of taxonomic signatures comprises, for each respective microbial taxon in the plurality of microbial taxa, a distinct set of k-mers determined from genomes of the microbial taxa, for each respective microbial taxon in the plurality of microbial taxa, the distinct set of k-mers is formed by removing k-mers that are present in more than one microbial taxa in the plurality of microbial taxa, based on a comparison across different microbial taxa, the plurality of microbial taxa are of the same taxonomic rank, each respective taxonomic signature in the metagenomic library of taxonomic signatures is at least 20 nucleotides long, and k is an integer between 5 and 100; the metagenomic library of taxonomic signatures comprises, for each respective microbial taxon in the plurality of microbial taxa, a distinct set of k-mers determined from genomes of the microbial taxa, for each respective microbial taxon in the plurality of microbial taxa, the distinct set of k-mers is formed by removing k-mers that are present in more than one microbial taxa in the plurality of microbial taxa, based on a comparison across different microbial taxa, the plurality of microbial taxa are of the same taxonomic rank, each respective taxonomic signature in the metagenomic library of taxonomic signatures is at least 20 nucleotides long, and k is an integer between 5 and 100; assaying for a presence of each of a plurality of biochemical activities in the heterogeneous microbial sample by mapping the nucleotide sequences to a nucleic acid library comprising open reading frames and identifying genes associated with the biochemical activities encoded by the open reading frame; and using a presence of a sequence signature for one or more microbial taxa in the plurality of microbial taxa to characterize a microbial composition of the heterogenous microbial sample.