Gut microbiota in hepatic encephalopathy, Japan, case-control
12 fecal samples from Japan, from patients with liver disease (hepatic encephalopathy/cirrhosis) and controls, studied for antibiotic (rifaximin) response using 16S rRNA and metagenomic sequencing in a case-control design. machine-written summary
12 samples · 12 runs · JP · Age unknown · 2022 · 14.51 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 96 sample values (collection date, country, health condition, health condition detail, latitude, location region, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC9315133 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
Antibiotic given as the study intervention (incl. eradication therapy design observational_with_procedure · population liver_disease · Rifaximin (nonabsorbable antibiotic) administration in HE patients
“their responses to rifaximin” — abstract:35429147 (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
6 of 6 people sampled more than once (12 samples; median 2, up to 2 per person). Schedule stated by the source: “Feces collected before RFX treatment and again 2-12 weeks after oral RFX administration (sample suffix -0 = pre, -1/-2 = post)”.
Genera, mean relative abundance over 11 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 | 0 | 0% | ||||
| country | 12 | 100% | 12 | |||
| health_condition | 12 | 100% | 12 | |||
| subject_id | 12 | 100% | 12 | |||
| collection_date | 12 | 100% | 12 | |||
| detailed_location | 12 | 100% | ||||
| health_condition_detail | 12 | 100% | 12 | |||
| latitude | 12 | 100% | 12 | |||
| location_region | 12 | 100% | 12 | |||
| longitude | 12 | 100% | 12 |
- Distinct responsiveness to rifaximin in patients with hepatic encephalopathy depends on functional gut microbial species. 2022 PMID 35429147 PMC9315133 own_data
Archive description
Hepatic encephalopathy is the end-stage complication of liver cirrhosis caused by hyperammonemia and concomitant neuropsychiatric disorders. This study aimed to identify specific species involved in hyperammonemia in HE patients through 16S rRNA gene amplicon and metagenomic sequencing analyses of the gut microbiota of HE patients.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.60. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.title · “hepatic encephalopathy patients”
- body site study.description · “gut microbiota of HE patients”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMD00276739 | collection_date | 2017 | R1 | 0.90 | biosample.attribute:collection_date | 2017 |
| SAMD00276739 | country | JP | R1 | 0.90 | sample.attr.geo_loc_name | Japan |
| SAMD00276739 | health_condition | liver_disease | R1 | 0.90 | biosample_attr | hepatic encephalopathy |
| SAMD00276739 | health_condition_detail | hepatic encephalopathy | R1 | 0.90 | sample.attr.host_disease_stat | hepatic encephalopathy |
| SAMD00276739 | latitude | 34.6400 | R1 | 0.90 | biosample.attribute:lat_lon | 34.64 N 135.51 E |
| SAMD00276739 | location_region | Osaka | R1 | 0.60 | biosample.attribute:lat_lon | 34.64 N 135.51 E |
| SAMD00276739 | longitude | 135.5100 | R1 | 0.90 | biosample.attribute:lat_lon | 34.64 N 135.51 E |
| SAMD00276739 | subject_id | R02 | R1 | 0.70 | sample.name_rule:attr:sample_name | R02-0 |
Sequencing
12 runs over 12 samples · mean 14.63 Gbp per run (median 14.51 Gbp, total 175.52 Gbp; 12 runs with a base count) · layout PAIRED 12 · platform ILLUMINA 12 · models Illumina HiSeq 2500 (12) · 92% of runs with a Sandpiper profile · first public 2022-04-11
Authors (12)
Yukawa-Muto Y first · Kamiya T · Fujii H · Mori H · Toyoda A · Sato I · Konishi Y · Hirayama A · Hara E · Fukuda S · Kawada N · Ohtani N last
Downloads
PRJDB10484.csv.gz (1.2 KB) · parquet (70.1 KB) — all 12 samples, every field with route and confidence · PRJDB10484_determinations.csv.gz (1.2 KB) — 96 evidence rows