US 11,773,455 B2
Method and system for microbiome-derived diagnostics and therapeutics infectious disease and other health conditions associated with antibiotic usage
Zachary Apte, San Francisco, CA (US); Jessica Richman, San Francisco, CA (US); Daniel Almonacid, San Francisco, CA (US); and Siavosh Rezvan Behbahani, San Francisco, CA (US)
Assigned to Psomagen, Inc., Rockville, MD (US)
Appl. No. 16/84,941
Filed by PSOMAGEN, INC., Rockville, MD (US)
PCT Filed Sep. 9, 2016, PCT No. PCT/US2016/051149
§ 371(c)(1), (2) Date Sep. 13, 2018,
PCT Pub. No. WO2017/044880, PCT Pub. Date Mar. 16, 2017.
Claims priority of provisional application 62/215,891, filed on Sep. 9, 2015.
Prior Publication US 2019/0100789 A1, Apr. 4, 2019
Int. Cl. C12Q 1/689 (2018.01); G16H 50/50 (2018.01); G16H 50/20 (2018.01); G16B 30/00 (2019.01); G16B 40/00 (2019.01); G16H 20/10 (2018.01); G16B 20/00 (2019.01); G16B 20/20 (2019.01); G16B 30/10 (2019.01); G16B 40/20 (2019.01); G16B 5/00 (2019.01); G16B 50/00 (2019.01); C12Q 1/6806 (2018.01); C12Q 1/6809 (2018.01); G06F 17/15 (2006.01); G06F 17/18 (2006.01)
CPC C12Q 1/689 (2013.01) [C12Q 1/6806 (2013.01); C12Q 1/6809 (2013.01); G06F 17/15 (2013.01); G06F 17/18 (2013.01); G16B 5/00 (2019.02); G16B 20/00 (2019.02); G16B 20/20 (2019.02); G16B 30/00 (2019.02); G16B 30/10 (2019.02); G16B 40/00 (2019.02); G16B 40/20 (2019.02); G16B 50/00 (2019.02); G16H 20/10 (2018.01); G16H 50/20 (2018.01); G16H 50/50 (2018.01); Y02A 90/10 (2018.01)] 9 Claims
 
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.