This directory contains processed data generated from 16S and shotgun analysis, with the full OTU relative or rarefied absolute abundance table provided in biom format. The rest are provided in csv format, and were used in relavant part of analysis as described below.
1.) human_16S.sampleinfo.csv
Metadata table consisting of patient samples, response groups, and RECIST scores.
2.) human_16S.even13190.abs.sig.csv
Rarefied absolute abundance of 63 human OTUs differentially abundant between 16S NR and R groups (42 samples in total, pre-treatment).
3.) human_16S.even13190.rel.sig.csv
Rarefied relative abundance of 63 human OTUs differentially abundant between 16S NR and R groups (42 samples in total, pre-treatment). This table was generated by taking the rarefied absolute abundance table and divide by the even sequencing depth (13190 reads). This file is essentially table S2 in the manuscript.
4.) human_16S.even13190.stats.sig.csv
Permutation test (QIIME v1.91 option nonparametric_t_test) stats of 63 human OTUs differentially abundant between 16S NR and R groups (42 samples in total, pre-treatment). This file is essentially table S4 in the manuscript.
5.) human_16S.even13190.abs.full.biom
Rarefied absolute abundance of full list of human OTUs assembled in 42 16S sequencing fecal samples. The biom format serves as the input for many tools. It can be converted to plain text format (e.g. tsv) using command biom convert -i table.biom -o table.txt --to-tsv
6.) human_16S.even13190.rel.full.biom
Rarefied relative abundance of full list of human OTUs assembled in 42 16S sequencing fecal samples. This table was generated by taking the rarefied absolute abundance table and divide by the even sequencing depth (13190 reads).
7.) human_16S_qPCR.csv
qPCR abundance of 10 validated human OTUs, including 8 bacteria more abundant in R, and 2 bacteria more abundant in NR. This file is essentially table S5 in the manuscript.
8.) human_shotgun.rel.full.csv
Relative abundance of full list of species profiled in 39 metagenomic shotgun sequencing human fecal samples.
9.) human_joint_evidence.csv
The biomarker summary table consisting of 16S qPCR score, OTU ratio, somatic mutational load, PDL1 and PD1 gene expression, and CD8+ IHC cell density in tumor.
10.) mouse_16S.sampleinfo.csv
Metadata table consisting of colonized mice samples, mice gender, patient donor, response groups, and mouse tumor growth groups.
11.) mouse_16S.even22560.abs.sig.csv
Rarefied absolute abundance of 519 mouse OTUs differentially abundant between slow and fast tumor growth group (91 samples in total, including TAC mice as control).
12.) mouse_16S.even22560.rel.sig.csv
Rarefied relative abundance of 519 mouse OTUs differentially abundant between human 16S NR and R groups (91 samples in total, including TAC mice as control). This table was generated by taking the rarefied absolute abundance table and divide by the even sequencing depth (22560 reads).
13.) mouse_16S.even22560.abs.full.biom
Rarefied absolute abundance of full list of OTUs assembled in 91 16S sequencing mouse samples.
14.) mouse_16S.even22560.rel.full.biom
Rarefied absolute abundance of full list of OTUs assembled in 91 16S sequencing mouse samples. This table was generated by taking the rarefied absolute abundance table and divide by the even sequencing depth (22560 reads).