Method and system for microbiome-derived diagnostics and therapeutics infectious disease and other health conditions associated with antibiotic usage

1. A method of determining an occurrence of a microbiome indicative of, or associated with, antibiotic usage, the method comprising,

providing a sample comprising bacteria from the individual human;

determining an amount(s) of one or more of selected bacterial taxon and gene sequence corresponding to selected gene functionality in the sample:

wherein the selected bacterial taxon consists of:

species selected from the group consisting of Dorea formicigenerans 39486 , Flavonifractor plautii 292800, Roseburia inulinivorans 360807 , Blautia faecis 871665 , Subdoligranulum variabile 214851 , Collinsella aerofaciens 74426, and Blautia luti 89014,

genus selected from the group consisting of Lachnospira 28050 , Collinsella 102106 , Subdoligranulum 292632 , Marvinbryantia 248744 , Dorea 189330 , Sarcina 1266, Roseburia 841 , Intestinibacter 1505657 , Anaerotruncus 244127 , Flavonifractor 946234 , Terrisporobacter 1505652 , Alistipes 239759 , Anaerostipes 207244, Faecalibacterium 216851, and Clostridium 1485,

family selected from the group consisting of Coriobacteriaceae 84107, Clostridiaceae 31979, Rikenellaceae 171550, Peptostreptococcaceae 186804, Ruminococcaceae 541000, and Sutterellaceae 995019,

order selected from the group consisting of Coriobacteriales 84999, Burkholderiales 80840, Clostridiales 186802, Selenomonadales 909929,

class selected from the group consisting of Betaproteobacteria 28216, Negativicutes 909932, and Clostridia 186801, wherein the selected gene functionality is selected from:

KEGG L2 functional group selected from the group consisting of Translation, Cell Growth and Death, Metabolism, Energy Metabolism, Environmental Adaptation, Replication and Repair, Poorly Characterized, and Signaling Molecules and Interaction, and

KEGG L3 functional group selected from the group consisting of Amino acid related enzymes, Aminoacyl—tRNA biosynthesis, Function unknown, Inorganic ion transport and metabolism, Ribosome, Cell cycle— Caulobacter , Amino acid metabolism, Pantothenate and COA biosynthesis, Translation factors, Alzheimer's disease, Others, Translation proteins, Ribosome Biogenesis, Thiamine metabolism, Homologous recombination, Terpenoid backbone biosynthesis, Tuberculosis, Carbon fixation in photosynthetic organisms, Cytoskeleton proteins, DNA repair and recombination proteins, Peptidoglycan biosynthesis, Ribosome biogenesis in eukaryotes, Nucleotide excision repair, Plant—pathogen interaction, Chromosome, and Protein export;

comparing the determined amount(s) to a condition signature having cut-off or probability values for amounts of the bacterial taxon and/or gene sequence for an individual having a microbiome indicative of antibiotic usage or an individual not having a microbiome indicative of antibiotic usage or not or both; and

determining the presence or absence of the microbiome indicative of antibiotic usage.

2. The method of claim 1 , wherein the determining comprises preparing DNA from the sample and performing nucleotide sequencing of the DNA.

3. The method of claim 1 , wherein the determining comprises deep sequencing bacterial DNA from the sample to generate sequencing reads,

receiving at a computer system the sequencing reads; and

mapping, with the computer system, the reads to bacterial genomes to determine whether the reads map to a sequence from the selected bacterial taxon or gene sequence corresponding to the selected gene functionality; and

determining a relative amount of different sequences in the sample that correspond to a sequence from the selected bacterial taxon or gene sequence corresponding to the selected gene functionality.

4. The method of claim 3 , wherein the deep sequencing is random deep sequencing.

5. The method of claim 3 , wherein the deep sequencing comprises deep sequencing of 16S rRNA coding sequences.

6. The method of claim 1 , wherein the method further comprises obtaining physiological, demographic or behavioral information from the individual human, wherein the condition signature comprises physiological, demographic or behavioral information; and

the determining comprises comparing the obtained physiological, demographic or behavioral information to corresponding information in the condition signature.

7. The method of claim 1 , wherein the sample is a fecal, blood, saliva, cheek swab, urine or bodily fluid from the individual human.

8. The method of claim 1 , further comprising determining that the individual human likely has a microbiome indicative of antibiotic usage; and

treating the individual human to ameliorate at least one symptom of the microbiome indicative of antibiotic usage.

9. The method of claim 8 , wherein the treating comprises administering a dose of one of more of the selected bacterial taxa to the individual human for which the individual human is deficient.