Fecal microbiota for CRC detection, France/Germany

Several bacterial species have been implicated in the development of colorectal carcinoma (CRC), but CRC-associated changes of fecal microbiota and their potential for cancer screening remain to be explored. Here we used metagenomic sequencing of fecal samples to identify taxonomic markers that distinguished CRC patients from tumor-free controls in a study population of 156 participants. Accuracy of metagenomic CRC detection was similar to the standard fecal occult blood test (FOBT) and when both approaches were combined, sensitivity improved >45% relative to the FOBT while maintaining its specificity. Accuracy of metagenomic CRC detection did not differ significantly between early and late-stage cancer and could be validated in independent patient and control populations (N=335) from different countries. CRC-associated changes in the fecal microbiome at least partially reflected microbial community composition at the tumor itself, indicating that observed gene pool differences may reveal tumor-related host-microbe interactions. Indeed, we deduced a metabolic shift from fiber degradation in controls to utilization of host carbohydrates and amino acids in CRC patients accompanied by an increase of lipopolysaccharide metabolism.

Classified as human gut / stool / blood / tissue / internal fluids shotgun DNA metagenome of adult and elderly by deterministic_prior with confidence 0.90. Assay shotgun_dna.

• host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
• body site study.title · “Potential of fecal microbiota for early”
• body site study.description · “the development of colorectal carcinoma (CRC), but”
• body site study.description · “CRC patients from tumor -free controls in”
• life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
• life stage sample.attr.age · “62 (n=98/199)”

1,290 runs over 199 samples · mean 0.82 Gbp per run (median 0.33 Gbp, total 1,060.62 Gbp; 1,290 runs with a base count) · layout PAIRED 645, SINGLE 645 · platform ILLUMINA 1,290 · models Illumina HiSeq 2000 (1,290) · 56% of runs with a Sandpiper profile · first public 2014-11-01

Tarracchini C first · Fontana F · Mancabelli L · Lugli GA · Alessandri G · Turroni F · Ventura M · Milani C last · Orihara K first · Yahagi K · Saito Y · Watanabe Y · Sasai T · Hara T · Tsukuda N · Oki K · Fujimoto J · Matsuki T last · De Biase R · Bocchio F · Viappiani A · De Conto F · Nouvenne A · Ticinesi A · Bussolati O · Meschi T · Cecchi R · van Sinderen D · Israel A first · Israel S · Weizman A · Ashkenazi S · Vinker S · Magen E · Merzon E last · Schroer HW first · Beghini F · Raygoza Garay JA · Christakis NA · Bosch DE last · Weilguny L first · Probul N · Ren Y · Pons N · Baumbach J · Almeida M last · Lee J first · Minot S · Dey N last

PRJEB6070.csv.gz (7.4 KB) · parquet (79.6 KB) — all 199 samples, every field with route and confidence · PRJEB6070_determinations.csv.gz (10.5 KB) — 1,587 evidence rows