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US 2021/0332418 A1Published application
Systems and methods for microbiome analysis
AssigneeViome, Inc.
InventorsMomchilo VUYISICH, Ally PERLINA, Guruduth S. BANAVAR, Helen MESSIER
Life of this patent
Estimating the term…
Abstract
Provided are methods balancing a gut microbiome. Methods involve sequencing nucleic acids from a sample to determine quantifies or activities of microorganisms Sequence information is used to generate functional activity scores for functional categories. These scores can be actionable. Methods also include generating recommendations involving administration of food, supplements, or medication to affect quantities or activities of microorganisms
Claims28
A method comprising:
- a) generating a dataset about a subject by:
- i) determining data from a gut microbiome from a subject by:
- (1) obtaining nucleic acids from a sample comprising gut microbiome from a subject;
- (2) obtaining sequence information representative of the nucleic acids;
- ii) determining from the sequence information, (A) quantitative measures of each of a plurality of different microbial taxa and (B) quantitative measures of activity of each of a plurality of different genes;
- b) determining from the dataset a functional activity score for at least one functional category;
- c) determining that the functional activity score is outside a reference range;
- and
- d) recommending alterations in a diet for, or altering a diet of, the subject to alter the gut microbiome, wherein altering the gut microbiome shifts the functional score toward or into the reference range.
6 more elements
A method comprising:
- a) determining for a subject a functional activity score for at least one functional category, where in the functional activity score is derived from a dataset comprising nucleic acid sequence-derived quantitative measures of each of a plurality of different microbial taxa and quantitative measures of activity of each of a plurality of different genes;
- b) determining that the functional activity score is outside a reference range;
- and
- c) transmitting to the subject a dietary item determined, when included in the diet of the subject, to alter the gut microbiome so as to shift the functional score toward or into the reference range.
1 more element
A method comprising:
- (a) receiving from the subject a sample comprising microbes from the subject's microbiome;
- (b) sequencing a transcriptome from the microbiome;
- (c) determining, from the sequence transcriptome, a functional utility score for each of one or more functional categories;
- (d) determining that the functional utility score is outside a reference range;
- (e) generating a dietary model including one or more dietary items which, when included in a diet of the subject, will move functional score toward or into the reference range;
- and
- (f) providing the dietary model or at least one of the dietary items to the subject.
4 more elements
A method of improving a health characteristic in a subject comprising:
- obtaining nucleic acids from a sample from the subject;
- obtaining sequence information representative of the nucleic acids;
- assigning a taxonomic designation to a portion of the nucleic acids having sequence signatures informative of the taxonomic designation;
- quantifying an amount of microorganisms in the sample corresponding to the taxonomic designation;
- comparing the quantity of microorganisms in the sample corresponding to the taxonomic designation to a reference value for the microorganism corresponding to the taxonomic designation;
- identifying a nutrient or medication that alters the growth of microorganisms corresponding to the taxonomic designation;
- and
- recommending or administering to the subject a food or supplement comprising the nutrient, or the medication that alters the growth of microorganisms corresponding to the taxonomic designation.
5 more elements
A method of improving a health characteristic in a subject comprising:
- obtaining nucleic acids from a sample from the subject;
- obtaining sequence information representative of the nucleic acids;
- quantifying an amount of the nucleic acids in the sample corresponding to a biochemical (metabolic or signaling) pathway activity;
- comparing the quantity of the biochemical activity in the sample to a reference value for the biochemical activity;
- identifying a nutrient that alters the amount of the biochemical activity in a gut of the subject;
- and
- recommending or administering to the subject a food or supplement containing the nutrient or medication that alters the amount of the biochemical activity in the gut of the subject.
4 more elements
A method of taxonomically assessing the biochemical activity of a heterogeneous sample comprising:
- obtaining ribonucleic acids from a heterogeneous sample;
- obtaining sequence information representative of the ribonucleic acids;
- assigning the ribonucleic acids to open reading frames;
- identifying biochemical activities in the sample consistent with the open reading frames;
- and
- identifying a recommendation consistent with the presence of the biochemical activity.
3 more elements
A method of assessing gut shedding in a subject comprising:
- obtaining nucleic acids from a stool sample;
- obtaining sequence information representative of the nucleic acids;
- assaying for a presence of a plurality of sequence signatures in the stool sample informative of a category of organisms;
- quantifying an amount of nucleic acid derived from the subject in the sample;
- quantifying an amount of nucleic acid derived from microorganisms in the sample;
- and
- assessing gut shedding in the subject by determining the proportion of nucleic acid derived from the subject to the proportion of nucleic acid derived from microorganisms.
4 more elements
A method of identifying antibiotic resistant microorganisms in a heterogeneous microbial sample from a subject comprising:
- obtaining ribonucleic acids from a heterogeneous microbial sample;
- obtaining sequence information representative of the ribonucleic acids;
- assaying for a presence of one or more sequence signatures in the heterogeneous microbial sample informative of a microorganism that is resistant to an antibiotic;
- and
- providing an effective amount of a different antibiotic to the subject to slow growth of the microorganism.
2 more elements
A method of treating a bacterial infection in a subject comprising:
- obtaining ribonucleic acids from a heterogeneous microbial sample from the subject;
- obtaining sequence information representative of the ribonucleic acids;
- assaying for a presence of a plurality of sequence signatures in the heterogeneous microbial sample informative of a microorganism that is sensitive to an antibiotic;
- and
- providing an effective amount of the antibiotic to the subject to slow growth of the microorganism.
2 more elements
A method of assessing a metabolism in a subject comprising:
- assaying for nucleic acids corresponding to taxa in a gut microbiome of the subject that enhance metabolism;
- and
- assaying for nucleic acids corresponding to taxa in the gut microbiome of the subject that reduce metabolism.
A method of assessing metabolism in a subject comprising:
- assaying for nucleic acids corresponding to taxa in a gut microbiome of the subject that enhance metabolism;
- and
- assaying for nucleic acids corresponding to taxa in the gut microbiome of the subject that reduce metabolism;
- and
- assessing metabolic activity in the subject in the subject based on the taxa in a gut microbiome of the subject that enhance metabolism and the taxa in the gut microbiome of the subject that reduce metabolism in the gut microbiome.
2 more elements
Dependencies are inferred from the claim text.