Supplementary Materials

Fecal microbiota transplant promotes response in immunotherapy-refractory melanoma patients

Erez N. Baruch, Ilan Youngster, Guy Ben-Betzalel, Rona Ortenberg, Adi Lahat, Lior Katz, Katerina Adler, Daniela Dick-Necula, Stephen Raskin, Naamah Bloch, Daniil Rotin, Liat Anafi, Camila Avivi, Jenny Melnichenko, Yael Steinberg-Silman, Ronac Mamtani, Hagit Harati, Nethanel Asher, Ronnie Shapira-Frommer, Tal Brosh-Nissimov, Yael Eshet, Shira Ben-Simon, Oren Ziv, Md Abdul Wadud Khan, Moran Amit, Nadim J. Ajami, Iris Barshack, Jacob Schachter, Jennifer A. Wargo, Omry Koren, Gal Markel, Ben Boursi

Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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  • Materials and Methods
  • Supplementary Text
  • Figs. S1 to S13
  • Tables S1 to S5 and S15
  • Captions for Tables S6 to S14
  • References
Table S6
Genus and Species levels profiling of FMT donors. Relative abundance of Genus and Species taxa were presented per donor, based on metagenomic sequencing. Data are presented in percentage, and each donor column for Genus/Species sums up to 100%. FMT – Fecal Microbiota Transplantation.
Table S7
Specific taxa which significantly differed in comparison of post-treatment microbiota compositions of the two donor-groups. Profiling differing taxa was based on metagenomic sequencing. The abundance of these taxa was compared between the two donorgroups using the ANalysis of Composition of Microbiomes (ANCOM) test. Negative mean abundance difference – taxa which were relatively more abundant in post-treatment stool samples of Donor#1-group recipients and Donor#1 himself; Positive mean abundance difference – taxa which were relatively more abundant in post-treatment stool samples of Donor#2-group recipients and Donor#2 herself. Statistical significance was defined as FDR q≤ 0.05.
Table S8
GO gene sets which were significantly enriched among the post-treatment microbiota compositions of the two donor-groups. Functional microbiota analysis was based on metagenomic sequencing. Microbiota genes were re-grouped to GO gene sets. The abundance of these gene sets was compared between the two donor-groups. Positive abundance difference – gene sets which were enriched in post-treatment stool samples of Donor#1-group recipients and Donor#1 himself; Negative abundance difference – pathways which were enriched in posttreatment stool samples of Donor#2-group recipients and Donor#2 herself. Statistical significance was defined as FDR q≤ 0.05. Pathways with log2 abundance difference <1 were filtered out of the analysis.
Table S9
Gene sets which were significantly enriched among all available post-treatment gut samples in comparison to their baseline. Gene sets were based on the Gene Ontology (GO) dataset. Statistical significance was defined as FDR q≤ 0.05. Up – gene sets which were enriched among all post-treatment gut samples; Down - gene sets which were enriched among all pretreatment gut samples. Recipient#2 did not consent to undergo repeated tumor and gut biopsies and was thus not included in the tissue analysis.
Table S10
Gene sets which were significantly enriched among Donor#1-group posttreatment gut samples in comparison to their baseline. Gene sets were based on the Gene Ontology (GO) dataset. Statistical significance was defined as FDR q≤ 0.05. Up – gene sets which were enriched among Donor#1-group post-treatment gut samples; Down - gene sets which were enriched among Donor#1-group pre-treatment gut samples.
Table S11
Gene sets which were significantly enriched among available Donor#2-group post-treatment gut samples in comparison to their baseline. Gene sets were based on the Gene Ontology (GO) dataset. Statistical significance was defined as FDR q≤ 0.05. Up – gene sets which were enriched among Donor#2-group post-treatment gut samples; Down - gene sets which were enriched among Donor#2-group pre-treatment gut samples. Recipient#2 did not consent to undergo repeated tumor and gut biopsies and was thus not included in the tissue analysis.
Table S12
Gene sets which were significantly enriched among all available post-treatment tumor samples in comparison to their baseline. Gene sets were based on the Gene Ontology (GO) dataset. Statistical significance was defined as FDR q≤ 0.05. Up – gene sets which were enriched among all post-treatment tumor samples; Down - gene sets which were enriched among all pre-treatment tumor samples. Recipient#2 did not consent to undergo repeated tumor and gut biopsies and was thus not included in the tissue analysis.
Table S13
Gene sets which were significantly enriched among Donor#1-group posttreatment tumor samples in comparison to their baseline. Gene sets were based on the Gene Ontology (GO) dataset. Statistical significance was defined as FDR q≤ 0.05. Up – gene sets which were enriched among Donor#1-group post-treatment tumor samples; Down - gene sets which were enriched among Donor#1-group pre-treatment tumor samples.
Table S14
Gene sets which were significantly enriched among available Donor#2-group post-treatment tumor samples in comparison to their baseline. Gene sets were based on the Gene Ontology (GO) dataset. Statistical significance was defined as FDR q≤ 0.05. Up – gene sets which were enriched among Donor#2-group post-treatment tumor samples; Down - gene sets which were enriched among Donor#2-group pre-treatment tumor samples. Recipient#2 did not consent to undergo repeated tumor and gut biopsies and was thus not included in the tissue analysis.
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