Method for predicting and improving treatment response to intestinal microbiome-based cancer immunotherapy and method for screening for candidate prebiotics

A method for generating microbial taxonomic profile data for predicting a treatment response to cancer immunotherapy comprising:

• performing metagenomic sequencing on a fecal sample from a patient to generate the microbial taxonomic profile data;
• wherein the cancer immunotherapy is anti-PD-1 treatment,
• wherein the microbial taxonomic profile data shows enrichment in the fecal sample from the patient of a strain according to NCBI (National Center for Biotechnology Information) phylogenetic classification of at least one of phylogenetic classification IDs:
• 1262796, 1262847, 1262772, 1262800, 1262811, 1262840, 1262822, 1262810, 1262839, 1262813, 1262784, 1262841, 1262823, 1262815, 1262812, 1262807, 1262799, 1262820, 1262788, 1262801, 1262789, 1896989, 1896977, 1896978, 1896979, 1896980, 1896981, 1896986, 1950810, 1950830, 1950862, 1950880, 1950887, 1950920, 1958817, or 1506 according to the NCBI phylogenetic classification;
• and
• wherein the enrichment of the at least one strain according to the NCBI phylogenetic classification is a biomarker for predicting the treatment response to the anti-PD-1 treatment.

A method for screening candidate prebiotics comprising:

• performing metagenomic sequencing on a fecal sample from a patient to generate microbial taxonomic profile data, wherein the patient has not received the candidate prebiotics;
• wherein the microbial taxonomic profile data shows enrichment in the fecal sample from the patient of the order TANB77 according to GTDB phylogenetic classification or taxa belonging to the order TANB77, or a strain according to GTDB phylogenetic classification of at least one of CAG-269 sp000431335 species, CAG-465 sp000433135 species, CAG-465 sp000433335 species, CAG-269 sp001916055 species, CAG-465 sp000433755 species, CAG-793 sp000433915 species, CAG-492 sp000434015 species, CAG-452 sp000434035 species, CAG-245 sp000434195 species, CAG-492 sp000434335 species, CAG-245 sp000435175 species, CAG-273 sp003507395 species, CAG-269 sp000435535 species, CAG-273 sp000435755 species, CAG-269 sp001916065 species, CAG-269 sp000437215 species, CAG-354 sp001915925 species, CAG-273 sp000437855 species, CAG-269 sp003525075 species, CAG-269 sp000438255 species, CAG-273 sp000438355 species, CAG-269 sp001915995 species, CAG-269 sp001916005 species, CAG-269 sp001916035 species, UBA1234 sp002308995 species, CAG-452 sp002314935 species, CAG-269 sp002372935 species, CAG-793 sp002393975 species, UBA1234 sp002404755 species, UBA7001 sp002449785 species, CAG-492 sp002633185 species, CAG-269 sp003518755 species, CAG-273 sp003534295 species, CAG-269 genus, CAG-492 genus, CAG-793 genus, CAG-452 genus, CAG-245 genus, CAG-273 genus, CAG-354 genus, UBA7001 genus, CAG-465 genus, UBA1234 genus, CAG-508 family, CAG-465 family, or UBA1234 family according to the GTDB phylogenetic classification, before administering the candidate prebiotics;
• administering the candidate prebiotics;
• and
• performing an additional metagenomic sequencing on a fecal sample from the patient to generate microbial taxonomic profile data after the administering of the candidate prebiotics;
• wherein the microbial taxonomic profile data shows differences in enrichment in the fecal sample from the patient of the order TANB77 or the taxa, or the at least one strain according to the GTDB phylogenetic classification before administering the candidate prebiotics with the enrichment of the order TANB77 or the taxa, or the at least one strain according to the GTDB phylogenetic classification after the administering of the candidate prebiotics;
• and
• wherein the candidate prebiotic increases the enrichment after the administration relative to before the administration.