Gut microbiome in NAFLD-cirrhosis and HCC, Sydney
90 gut metagenome samples from adults in Sydney, Australia, comparing NAFLD-related cirrhosis with and without hepatocellular carcinoma to healthy controls, in a case-control design examining microbiome/metabolome effects on peripheral immune response. machine-written summary
90 samples · 90 runs · AU · Adult · 2020 · 9.51 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 280 sample values (collection date, country, latitude, location locality, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 143 sample values (country, subject id) · PMC7794332 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 32 sample values (country) · from MicrobeAtlas |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 82 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 90 | 100% | ||||
| country | 90 | 100% | 5 | 32 | 53 | |
| health_condition | 0 | 0% | ||||
| subject_id | 90 | 100% | 90 | |||
| collection_date | 90 | 100% | 90 | |||
| latitude | 90 | 100% | 90 | |||
| longitude | 90 | 100% | 90 | |||
| detailed_location | 5 | 6% | ||||
| location_locality | 5 | 6% | 5 |
- Gut microbiota impact on the peripheral immune response in non-alcoholic fatty liver disease related hepatocellular carcinoma. 2021 PMID 33420074 PMC7794332 own_data
Archive description
The project examines the direct effect of the microbiome on the peripheral immune response in patients with NAFLD-HCC. The project employs shotgun metagenomics and metabolomics to present novel insights to the structure, function and metabolomic capability of the gut microbiome in patients with NAFLD-cirrhosis, with and without HCC compared to healthy controls. Next, we examine in an ex-vivo cell culture model the effect of NAFLD-HCC-associated microbiome and metabolome on the peripheral immune response.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.65. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “structure, function and metabolomic capability of the gut microbiome”
- life stage study.description · “patients with NAFLD-cirrhosis, with and without HCC”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN15589066 | collection_date | 2017 | R1 | 0.90 | biosample.attribute:collection_date | 2017 |
| SAMN16709256 | country | AU | R1 | 0.90 | sample.attr.geo_loc_name | Australia: Sydney |
| SAMN15589066 | country | AU | R2 | 0.65 | external.microbeatlas source | lat_lon: 33.52 S 151.20 E |
| SAMN15589068 | country | AU | R3 | 0.70 | paper.fulltext.methods | Sydney Local Health District Human Research Ethics Committee |
| SAMN15589066 | latitude | -33.5200 | R1 | 0.90 | biosample.attribute:lat_lon | 33.52 S 151.20 E |
| SAMN16709256 | location_locality | Sydney | R1 | 0.85 | biosample.attribute:geo_loc_name | Australia: Sydney |
| SAMN15589066 | longitude | 151.2000 | R1 | 0.90 | biosample.attribute:lat_lon | 33.52 S 151.20 E |
| SAMN15589066 | subject_id | SAMN15589066 | R3 | 0.70 | design.one_sample_per_subject:fulltext | A total of 90 subjects were recruited in the study; 32 with NAFLD-HCC, 28 with NAFLD-cirrhosis and 30 non-NAFLD control. |
Sequencing
90 runs over 90 samples · mean 9.40 Gbp per run (median 9.51 Gbp, total 846.38 Gbp; 90 runs with a base count) · layout PAIRED 90 · platform ILLUMINA 90 · models Illumina NovaSeq 6000 (90) · 91% of runs with a Sandpiper profile · first public 2020-11-21
Authors (18)
Behary J first · Amorim N · Jiang XT · Raposo A · Gong L · McGovern E · Ibrahim R · Chu F · Stephens C · Jebeili H · Fragomeli V · Koay YC · Jackson M · O'Sullivan J · Weltman M · McCaughan G · El-Omar E · Zekry A last
Downloads
PRJNA647523.csv.gz (3.3 KB) · parquet (73.9 KB) — all 90 samples, every field with route and confidence · PRJNA647523_determinations.csv.gz (4.2 KB) — 455 evidence rows