Compositions and methods for characterizing a complex biological sample

A method of characterizing a complex biological sample, the method comprising:

• (a) contacting polynucleotides derived from the complex biological sample with the set of probes generated in claim 111, or a subset of such probes, under conditions that permit hybridization of the probes to the polynucleotides, thereby forming polynucleotide/probe complexes, wherein each probe is coupled to a binding member;
• (b) contacting the polynucleotide/probe complexes with a capture molecule fixed to a solid support, wherein the capture molecule specifically binds the binding member of the probe, thereby enriching polynucleotides of the complex biological sample;
• and
• (c) characterizing the enriched polynucleotides.

A method for generating a set of probes for use in pan-genomic or pan-transcriptomic sequencing of polynucleotides derived from organisms present in a microbiome, the method comprising:

• (a) identifying a plurality of orthogroup clusters of gene sequences within a set of genomes derived from the organisms, wherein the organism are present in a microbiome;
• (b) identifying a plurality of gene clusters within the orthogroup clusters, wherein the gene sequences within each of the gene clusters share at least about 80% nucleotide sequence identity;
• and
• (c) generating a set of probes, wherein each probe within the set comprises from about 50 to about 85 nucleotides, wherein each probe is complementary to at least about 25 base pairs of a gene sequence present in the gene clusters identified in (b), wherein the probes collectively cover at least about 50% of all gene sequences in the gene clusters, and wherein the set excludes probes having 50 or more contiguous nucleotides that are identical to a set of reference sequences, and wherein coverage of each probe is determined using a cover extension of about 20 bp.