Comparative Analysis of Urinary, Bladder Tissue, and Stool Microbiota in Bladder Cancer Using Shotgun Metagenomics
Urine has been investigated as a non-invasive biomarker for bladder cancer (BCa) due to its direct contact with the bladder mucosa. This study aimed to determine whether the catheterized urine microbiome reflects bladder tissue microbial composition and functional potential, and to develop a predictive model to estimate tissue microbiota from urine profiles. Matched bladder tissue (n=79), catheterized urine (n=79), and stool (n=17) samples were collected from BCa patients under sterile conditions. DNA was extracted, followed by shotgun metagenomic sequencing on an Illumina NovaSeq 6000 using 150 bp paired-end reads. Bioinformatic analyses were performed to characterize microbial composition and metabolic pathways. Tissue and urine microbiomes showed similar richness and evenness, with high compositional concordance (76.5% species overlap), while stool was compositionally distinct. Functional pathway profiles showed higher correlations and lower variability for tissue-urine than for other pairings. The tissue-urine concordance was consistent across patient subgroups stratified by sex and invasion status. A Ridge regression model predicted tissue microbiome composition from urine profiles with high accuracy at the phylum (R2=0.907) and class (R2=0.834) levels. These findings support catheterized urine as a reliable surrogate for bladder tissue microbiome profiling in BCa.
Urine has been investigated as a non-invasive biomarker for bladder cancer (BCa) due to its direct contact with the bladder mucosa. This study aimed to determine whether the catheterized urine microbiome reflects bladder tissue microbial composition and functional potential, and to develop a predictive model to estimate tissue microbiota from urine profiles. Matched bladder tissue (n=79), catheterized urine (n=79), and stool (n=17) samples were collected from BCa patients under sterile conditions. DNA was extracted, followed by shotgun metagenomic sequencing on an Illumina NovaSeq 6000 using 150 bp paired-end reads. Bioinformatic analyses were performed to characterize microbial composition and metabolic pathways. Tissue and urine microbiomes showed similar richness and evenness, with high compositional concordance (76.5% species overlap), while stool was compositionally distinct. Functional pathway profiles showed higher correlations and lower variability for tissue-urine than for other pairings. The tissue-urine concordance was consistent across patient subgroups stratified by sex and invasion status. A Ridge regression model predicted tissue microbiome composition from urine profiles with high accuracy at the phylum (R2=0.907) and class (R2=0.834) levels. These findings support catheterized urine as a reliable surrogate for bladder tissue microbiome profiling in BCa.
Gwangju Institute of Science and Technology