US 2026/0275426 A1 · METHODS OF CLASSIFYING AND TREATING INFLAMMATORY BOWEL DISEASE

Abstract

Embodiments of the disclosure encompass methods and compositions for treating and/or identifying subjects having Inflammatory Bowel Disease (IBD). In certain embodiments, methods include measuring taxa occurrence frequencies in at least one microbiome sample from a subject suspected or having or being at risk for having IBD when certain taxa are enriched in the microbiome and/or when certain taxa are deficient in the microbiome, and particularly upon classification of their microbiome based on a taxa enrichment profile. In certain embodiments, an individual is determined to be a suitable donor for fecal microbiota transplant or is determined not to be a suitable donor for FMT based on classification of the taxa profile of their microbiome.

Claims93

Dependent claims

A method of treating and optionally diagnosing Inflammatory Bowel Disease (IBD) in a subject, comprising:

a) measuring taxa occurrence frequencies in at least one microbiome sample from a subject,
b) determining that the subject has or is at risk of developing IBD when the microbiome sample comprises enrichment in taxa Bacteroides, Blautia, and Lachnospiraceae, and depletion of taxa Faecalibacterium, Bifidobacteria, and Eubacteria, and
c) administering a therapy for the IBD.

A kit, comprising:

(a) three or more bacteria species representative of at least three or more of the following listed bacterial taxa:
Bacteroides, Blautia, Faecalibacterium, Unclassified_071, Alistipes, Ruminococcus, Parabacteroides, Unclassified_072, Unclassified_075, Lachnospiraceae incertae sedis, Roseburia, Anaerostipes, Not_Available_2, Fusicatenibacter, Dorea, Coprococcus, Bifidobacterium, Eubacterium, Streptococcus, Ruminococcus2, Lactobacillus, Gemmiger, Romboutsia, Unclassified_087, Odoribacter, Akkermansia, Unclassified_123, Bilophila, Flavonifractor, Ruthenibacterium, Barnesiella, Parasutterella, Lachnoclostridium, Agathobaculum, Intestinibacter, Erysipelatoclostridium, Prevotella, Phascolarctobacterium, Clostridium IV, and Unclassified_037;
(b) three or more bacteria species representative of at least three or more of the following listed bacterial taxa:
Blautia, Faecalibacterium, Bifidobacterium, Unclassified_071, Ruminococcus, Lachnospiraceae incertae sedis, Unclassified_075, Bacteroides, Dorea, Unclassified_072, Anaerostipes, Not_Available 2, Fusicatenibacter, Coprococcus, Streptococcus, Romboutsia, Roseburia, Gemmiger, Alistipes, Collinsella, Agathobaculum, Ruminococcus2, Intestinibacter, Unclassified 087, Parabacteroides, Unclassified_074, Clostridium, Eubacterium, Lactobacillus, Unclassified 083, Turicibacter, Akkermansia, Dialister, Adlercreutzia, Schaalia, Erysipelatoclostridium, Clostridium sensu stricto, Not_Available_5, Ruthenibacterium, and Clostridium IV;
and/or
(c) three or more bacteria species representative of at least three or more of the following listed bacterial taxa:
Prevotella, Bacteroides, Faecalibacterium, Unclassified_071, Blautia, Roseburia, Unclassified_072, Unclassified_075, Ruminococcus, Parabacteroides, Lachnospiraceae incertae sedis, Coprococcus, Dorea, Alistipes, Fusicatenibacter, Anaerostipes, Bifidobacterium, Unclassified_087, Eubacterium, Lactobacillus, Gemmiger, Streptococcus, Unclassified_037, Romboutsia, Ruminococcus2, Unclassified_083, Odoribacter, Sutterella, Not_Available 2, Bilophila, Barnesiella, Dialister, Butyricimonas, Clostridium, Intestinibacter, Paraprevotella, Haemophilus, Clostridium IV, Phascolarctobacterium, and Flavonifractor.

4 more elements

A method of diagnosing IBD in a subject, comprising:

a) measuring taxa occurrence frequencies in at least one microbiome sample from a subject suspected of having IBD or at risk for having IBD;
b) classifying the subject microbiome into one of five Clusters, wherein each Cluster is associated with a taxa enrichment profile, wherein a subject having a microbiome associated with Cluster 1 or Cluster 3 is determined to have IBD or be at risk for having IBD,
wherein
(I) Cluster 1 is enriched at least in, or only in, Bacteroides, Blautia, Lachnospiraceae, and unclassified taxa;
or
Cluster 1 is enriched in 1 or more of the following listed bacterial taxa:
Bacteroides, Blautia, Unclassified_071, Faecalibacterium, Unclassified_075, Unclassified_072, Anaerostipes, Lachnospiraceae incertae sedis, Parabacteroides, Roseburia, Alistipes, Streptococcus, Ruminococcus, Dorea, Bifidobacterium, Fusicatenibacter, Unclassified_087, Ruminococcus2, Coprococcus, Flavonifractor, Eubacterium, Lachnoclostridium, Clostridium XIVa, Dialister, Lactobacillus, Erysipelatoclostridium, Unclassified_083, Unclassified_037, Intestinibacter, Veillonella, Unclassified 129, Romboutsia, Ruthenibacterium, Collinsella, Unclassified_123, Unclassified 074, Not_Available_2, Prevotella, Parasutterella, and Clostridium;
and
(II) Cluster 3 is enriched at least in, or only in, Bacteroides, Blautia, Enterobacteriaceae, Streptococcus, and unclassified taxa;
or
Cluster 3 is enriched in 1 or more of the following listed bacterial taxa:
Bacteroides, Blautia, Streptococcus, Unclassified_123, Unclassified_071, Unclassified_129, Veillonella, Lactobacillus, Erysipelatoclostridium, Unclassified_072, Lachnoclostridium, Bifidobacterium, Enterococcus, Anaerostipes, Lachnospiraceae incertae sedis, Clostridium XIVa, Unclassified_087, Clostridium, Faecalibacterium, Parabacteroides, Unclassified_074, Unclassified_075, Flavonifractor, Unclassified 064, Roseburia, Dialister, Unclassified_132, Intestinibacter, Prevotella, Clostridium XVIII, Alistipes, Not_Available 2, Unclassified_083, Akkermansia, Haemophilus, Fusobacterium, Romboutsia, Ruminococcus2, Fusicatenibacter, and Clostridium sensu stricto.

9 more elements

Dependencies are inferred from the claim text.

Methods of classifying and treating inflammatory bowel disease

Life of this patent

Methods of classifying and treating inflammatory bowel disease

Life of this patent

Abstract

Claims93