Gut metagenomics across seven cancers vs controls, Warsaw

The key association between gut dysbiosis and cancer is already known. Here, we used whole-genome shotgun sequencing (WGS) and gas chromatography/mass spectrometry (GC/MS) to conduct metagenomic and metabolomic analyses to identify common and distinct taxonomic configurations among 40, 45, 71, 34, 50, 60, and 40 patients with colorectal cancer, stomach cancer, breast cancer, lung cancer, melanoma, lymphoid neoplasms and acute myeloid leukemia (AML), respectively, and compared the data with those from sex- and age-matched healthy controls (HC). Alpha-diversity differed only between the lymphoid neoplasm and AML groups and their respective HC, while Geta-diversity differed between all groups and their HC. Of 203 unique species, 179 and 24 were under- and over-represented, respectively, in the case groups compared with HC. Of these, Faecalibacillus intestinalis was under-represented in each of the seven groups studied, Anaerostipes hadrus was under-represented in all but the stomach cancer group, and 22 species were under-</p><p>represented in the remaining five case groups. There was a marked reduction in the gut microbiome cancer index in all case groups except the AML group. Of the short-chain fatty acids and amino acids tested, the relative concentration of formic acid was significantly higher in each of the case groups than in HC, and the abundance of seven species of Faecalibacterium correlated negatively with most amino acids and formic acid, and positively with the levels of acetic, propanoic, and butanoic acid. In conclusion, we found more differences than similarities between the studied malignancy groups, with large variations in diversity, taxonomic/metabolomic profiles, and functional assignments. While the results obtained may demonstrate trends rather than objective differences that correlate with different types of malignancy, the newly developed gut microbiota cancer index did distinguish most of the cancer cases from HC. We believe that these data are a promising step forward in the search for new diagnostic and predictive tests to assess intestinal dysbiosis among cancer patients.

Classified as human gut / stool shotgun DNA metagenome of adult and elderly by opus_adjudicated with confidence 0.70. Assay shotgun_dna.

• host run.host_tax_id · “9606”
• host study.description · “patients with colorectal cancer”
• body site study.title · “fecal Faecalibacillus intestinalis”
• life stage sample.attr.host_age · “67 (n=231/387)”
• life stage sample.attr.host_age · “65 (n=143/387)”

387 runs over 387 samples · mean 4.07 Gbp per run (median 3.72 Gbp, total 1,574.34 Gbp; 387 runs with a base count) · layout PAIRED 387 · platform ILLUMINA 387 · models Illumina NovaSeq 6000 (387) · 90% of runs with a Sandpiper profile · first public 2024-10-18 – 2024-12-04

Kulecka M first · Czarnowski P · Bałabas A · Turkot M · Kruczkowska-Tarantowicz K · Żeber-Lubecka N · Dąbrowska M · Paszkiewicz-Kozik E · Walewski J · Ługowska I · Koseła-Paterczyk H · Rutkowski P · Kluska A · Piątkowska M · Jagiełło-Gruszfeld A · Tenderenda M · Gawiński C · Wyrwicz L · Borucka M · Krzakowski M · Zając L · Kamiński M · Mikula M · Ostrowski J last

PRJNA1116523.csv.gz (11.5 KB) · parquet (85.1 KB) — all 387 samples, every field with route and confidence · PRJNA1116523_determinations.csv.gz (17.7 KB) — 2,964 evidence rows