Metagenomes in European NAFLD Registry case-control cohort

Non-alcoholic fatty liver disease (NAFLD) is the most common chronic liver disease in developed countries, and its prevalence continues to rise in association with the global obesity and diabetes pandemic. While liver biopsy is recognized as the diagnostic standard, it is assumed that this condition is underdiagnosed and that there is a need for new non-invasive methods of NAFLD diagnosis. Murine studies with fecal transfer experiment suggest that the gut microbiota plays a role in NAFLD development. Moreover, with the emergence of next generation sequencing technologies, the microbiome hypothesis opens the door to use gut microbial signatures to diagnose NAFLD. We have analyzed the metagenomes of a cohort of 173 liver-biopsied patients (20 controls, 22 NAFLD, and 131 NASH) derived from the European NAFLD Registry. 16 microbial species are associated with different grades of the NAFLD spectrum, 5 with NAFLD, 6 with fibrosis, and 5 with both phenotypes. Among them, the abundance of species from the genus Alistipes, Oscillibacter were particularly modified. Functional exploration revealed a reduction in the number of microbial genes associated with amino acid degradation pathways, sugar catabolism, and the production of butyrate in the NAFLD progression grades. Finally, applying a recently developed machine learning approach (Predomics), we revealed that some microbial signatures provide predictive potential (AUROC values from 0.76 to 0.86), paving the way for the development of non-invasive tool using microbial signatures for NASH diagnosis.

Classified as human gut / stool / blood / tissue / internal fluids shotgun DNA metagenome of adult 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.description · “Murine studies with fecal transfer experiment suggest”
• body site external_curation.infant_catalog · “body_site_call gut”
• body site study.description · “Non-alcoholic fatty liver disease (NAFLD) is”
• life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”

173 runs over 173 samples · mean 7.36 Gbp per run (median 7.22 Gbp, total 1,273.71 Gbp; 173 runs with a base count) · layout PAIRED 173 · platform ILLUMINA 173 · models Illumina HiSeq 2500 (158), Illumina NovaSeq 6000 (15) · 91% of runs with a Sandpiper profile · first public 2023-07-12

He N first · Wang H · Yang Z · Li H · Liu B · Chen K · Wu Z · Zhao X · Liang H · Wang M · Li X · Zhong Y · Zhang H · Xiao L · Kristiansen K · Peng J · Zou Y · Li S last · Guo J first · Xiang Zw · Hu Ff · Zhang Sx · Han Wj · Ding X · Wang X · Ye Ml · Chen Jh · Rao T · Wu Ll · Lian Gh · Zhang W · Huang Y · Chen Y last

PRJEB55534.csv.gz (5.2 KB) · parquet (76.8 KB) — all 173 samples, every field with route and confidence · PRJEB55534_determinations.csv.gz (5.0 KB) — 672 evidence rows