Method and system for characterization for appendix-related conditions associated with microorganisms

Patent metadata

Field	Value
Publication number	US-2018342322-A1
Application number	US-201816039276-A
Country	US
Kind code	A1
Filing date	Jul 18, 2018
Priority date	Oct 21, 2014
Publication date	Nov 29, 2018
Grant date	—

Abstract

Embodiments of a method and/or system for characterizing one or more appendix-related conditions can include determining a microorganism dataset associated with a set of subjects; and/or performing a characterization process associated with the one or more appendix-related conditions, based on the microorganism dataset, where performing the characterization process can additionally or alternatively include performing an appendix-related characterization process for the one or more appendix-related conditions, and/or determining one or more therapies.

First claim

We claim:

1 . A method for characterizing an appendix-related condition associated with microorganisms, the method comprising:
determining a microorganism sequence dataset associated with a set of subjects, based on microorganism nucleic acids from samples associated with the set of subjects, wherein the samples comprise at least one sample associated with the appendix-related condition; collecting, for the set of subjects, supplementary data associated with the appendix-related condition; determining a set of microbiome features comprising at least one of a set of microbiome composition features and a set of microbiome functional features, based on the microorganism sequence dataset; generating an appendix-related characterization model based on the supplementary data and the set of microbiome features, wherein the appendix-related characterization model is associated with the appendix-related condition; determining an appendix-related characterization for a user for the appendix-related condition based on the appendix-related characterization model; and providing a therapy to the user for facilitating improvement of the appendix-related condition, based on the appendix-related characterization.

2 . The method of claim 1 , wherein the samples comprise first site-specific samples associated with a gut site, wherein determining the set of microbiome features comprises determining, based on the microorganism sequence dataset, the set of microbiome composition features comprising first site-specific composition features associated with the gut site and at least one of Neisseriaceae (family), Neisseria mucosa (species), Aggregatibacter aphrophilus (species), Bacteroides uniformis (species), Bacteroides vulgatus (species), Parabacteroides distasonis (species), Megasphaera (genus), Proteobacteria (phylum), Micrococcaceae (family), Streptococcus thermophilus (species), Streptococcus parasanguinis (species), Gemella (genus), Clostridium (genus), Actinomyces odontolyticus (species), Actinomycetales (order), Actinomycetaceae (family), Betaproteobacteria (class), Gemella morbillorum (species), Rothia (genus), Lactobacillus crispatus (species), Pseudomonadales (order), Oxalobacteraceae (family), Burkholderiales (order), Gemella sp. 933-88 (species), Micrococcales (order), Bacteroides acidifaciens (species), Mogibacterium (genus), Bacteroides sp. AR20 (species), Bacteroides sp. AR29 (species), Burkholderiaceae (family), Erysipelotrichaceae (family), Xanthomonadales (order), Pseudomonadaceae (family), Actinomyces sp. oral strain Hal-1065 (species), Roseburia intestinalis (species), Porphyromonadaceae (family), Shuttleworthia (genus), Clostridia (class), Clostridiales (order), Peptostreptococcaceae (family), Peptococcaceae (family), Carnobacteriaceae (family), Dialister sp. E2_20 (species), Neisseriales (order), Megasphaera genomosp. C1 (species), Moryella (genus), Synergistetes (phylum), Erysipelotrichia (class), Erysipelotrichales (order), Clostridiales Family XIII. Incertae Sedis (family), Roseburia sp. 11SE39 (species), Bacteroides sp. D22 (species), Synergistia (class), Synergistales (order), Synergistaceae (family), Lactobacillus sp. TAB-22 (species), Flavonifractor (genus), Sutterellaceae (family), Anaerostipes sp. 5_1_63FAA (species), Streptococcus sp. 2011_Oral_MS_A3 (species), Veillonella sp. 2011_Oral_VSA_D3 (species), Finegoldia sp. S9 AA1-5 (species), Fretibacterium (genus), Staphylococcus sp. 334802 (species), Peptoclostridium (genus), Intestinibacter (genus), Acinetobacter (genus), Klebsiella (genus), Bacteroides thetaiotaomicron (species), Butyrivibrio (genus), Fusobacterium necrogenes (species), Herbaspirillum (genus), Herbaspirillum seropedicae (species), Pediococcus (genus), Finegoldia magna (species), Blautia hansenii (species), Enterococcus faecalis (species), Lactococcus lactis (species), Bacillus (genus), Clostridioides difficile (species), Blautia coccoides (species), Erysipelatoclostridium ramosum (species), Weissella confusa (species), Lactobacillus plantarum (species), Lactobacillus paracasei (species), Bifidobacterium adolescentis (species), Bifidobacterium breve (species), Bifidobacterium dentium (species), Bifidobacterium animalis (species), Bifidobacterium pseudocatenulatum (species), Bacteroides ovatus (species), Peptoniphilus lacrimalis (species), Anaerococcus vaginalis (species), Rahnella (genus), Bilophila wadsworthia (species), Sneathia sanguinegens (species), Succiniclasticum (genus), Sporobacter (genus), Pseudobutyrivibrio ruminis (species), Weissella (genus), Bacteroides stercoris (species), Lactobacillus rhamnosus (species), Pantoea (genus), Holdemania (genus), Holdemania filiformis (species), Thermoanaerobacterales (order), Bifidobacterium gallicum (species), Bifidobacterium pullorum (species), Leuconostocaceae (family), Eggerthella lenta (species), Papillibacter (genus), Anaerostipes caccae (species), Pseudoflavonifractor capillosus (species), Anaerovorax (genus), Parasporobacterium (genus), Parasporobacterium paucivorans (species), Oscillospira (genus), Oscillospira guilliermondii (species), Actinomyces turicensis (species), Anaerosinus (genus), Sneathia (genus), Brevibacterium paucivorans (species), Lactobacillus sp. CR-609S (species), Thermoanaerobacteraceae (family), Bacillaceae (family), Gelria (genus), Acidobacteriales (order), Bacteroides massiliensis (species), Rhodocyclales (order), Anaerofustis stercorihominis (species), Alistipes finegoldii (species), Oscillospiraceae (family), Peptoniphilus sp. 2002-38328 (species), Hespellia (genus), Bacteroides sp. 35AE37 (species), Marvinbryantia (genus), Anaerosporobacter mobilis (species), Anaerofustis (genus), Catabacter (genus), Flavonifractor plautii (species), Proteiniphilum (genus), Roseburia faecis (species), Streptococcus sp. S16-11 (species), Bacteroides sp. 4072 (species), Alistipes shahii (species), Bacteroides intestinalis (species), Lactonifactor longoviformis (species), Bifidobacterium tsurumiense (species), Bacteroides dorei (species), Bacteroides xylanisolvens (species), Cronobacter (genus), Alloscardovia (genus), Alloscardovia omnicolens (species), Lactonifactor (genus), Catabacteriaceae (family), Adlercreutzia equolifaciens (species), Adlercreutzia (genus), Alistipes sp. EBA6-25c12 (species), Bacteroides sp. EBA5-17 (species), Oscillibacter (genus), Gordonibacter pamelaeae (species), Alistipes sp. NML05A004 (species), Parasutterella excrementihominis (species), Mitsuokella sp. DJF_RR21 (species), Butyricimonas (genus), Bifidobacterium stercoris (species), Alistipes indistinctus (species), Gordonibacter (genus), Anaerostipes hadrus (species), Klebsiella sp. B12 (species), Alistipes sp. RMA 9912 (species), Anaerosporobacter (genus), Bacteroides faecis (species), Blautia sp. Ser5 (species), Bacteroides chinchillae (species), Bilophila sp. 4_1_30 (species), Caldicoprobacteraceae (family), Enterobacter sp. UDC345 (species), Bifidobacterium biavatii (species), Peptoniphilus sp. 1-14 (species), Alistipes sp. HGB5 (species), Bacteroides sp. SLC1-38 (species), Lactobacillus sp. Akhmrol (species), Klebsiella sp. SOR89 (species), Enterococcus sp. C6 I11 (species), Pseudoflavonifractor (genus), Bacteroides sp. dnLKV9 (species), Megasphaera sp. BV3C16-1 (species), Faecalibacterium sp. canine oral taxon 147 (species), Varibaculum sp. CCUG 45114 (species), Butyricimonas sp. 214-4 (species), Anaerostipes rhamnosivorans (species), Negativicoccus sp. S5-A15 (species), [ Collinsella] massiliensis (species), Corynebacterium sp. jw37 (species), Roseburia sp. 499 (species), Dialister sp. S7MSR5 (species), Anaero

Assignees

• Ubiome Inc

Inventors

• Apte Zachary
• Richman Jessica
• Almonacid Daniel
• Ortiz Rodrigo
• Valdivia Catalina
• Pedroso Inti
• Tapia Paz

Classifications

• G16H10/60

  for patient-specific data, e.g. for electronic patient records · CPC title

• G06F19/28

  Physics · mapped topic

• G16H50/20 Primary

  for computer-aided diagnosis, e.g. based on medical expert systems · CPC title

• G16B50/00

  ICT programming tools or database systems specially adapted for bioinformatics · CPC title

• G16H20/00

  ICT specially adapted for therapies or health-improving plans, e.g. for handling prescriptions, for steering therapy or for monitoring patient compliance · CPC title