Gut microbiome, multiple chemical sensitivity, Japan
Cross-sectional study of 30 fecal samples from Japanese patients with multiple chemical sensitivity/idiopathic environmental intolerance, profiled by MiSeq shotgun metagenomic sequencing. machine-written summary
30 samples · 30 runs · JP · Age unknown · 2023 · 1.71 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 60 sample values (collection date, country) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 120 sample values (antibiotic exposure, location site, sex, subject id) · PMC10926566 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 60 sample values (health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 30 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 | 30 | 100% | 30 | |||
| health_condition | 30 | 100% | 30 | |||
| subject_id | 30 | 100% | 30 | |||
| antibiotic_exposure | 30 | 100% | 30 | |||
| collection_date | 30 | 100% | 30 | |||
| detailed_location | 30 | 100% | ||||
| health_condition_detail | 30 | 100% | 30 | |||
| location_site | 30 | 100% | 30 | |||
| sex | 30 | 100% | 30 |
- Metagenomic gut microbiome analysis of Japanese patients with multiple chemical sensitivity/idiopathic environmental intolerance. 2024 PMID 38468206 PMC10926566 own_data
Archive description
Feces samples of 30 Japanese patients with multiple chemical sensitivity/Idiopathic Environmental Intolerance were collected. The fecal DNA samples were sequenced using the MiSeq (Illumina, Inc. San Diego, CA, USA). For microbial genome/species assignment of the metagenomic reads, 500,000 high-quality metagenomic reads per individual were mapped to reference genomes using Bowtie232 (v2.2.1). For each individual, the filter-passed MiSeq reads were assembled using MEGAHIT (v1.2.4). Prodigal (v2.6.3) was used to predict protein-coding genes (greater than or equal to 100 bp) in contigs (greater than or equal to 500 bp) and singletons (greater than or equal to 300 bp). The non-redundant genes were functionally assigned by alignments against the Kyoto Encyclopedia of Genes and Genomes (KEGG) database (release 2019-10-07) using DIAMOND (e-value less than or equal to 1.0e-5) [20] to obtain KEGG orthologies (KOs).
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.80. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “Gut Microbiome Analysis of Japanese Patients”
- body site run.scientific_name · “human gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMD00633985 | antibiotic_exposure | no | R3 | 0.70 | paper.body.methods_results | receiving treatment with antibiotics and/or proton pump inhibitors (PPIs) within the last six months |
| SAMD00633985 | collection_date | 2018-01-21 | R1 | 0.90 | biosample.attribute:collection_date | 2018-01-21 |
| SAMD00633985 | country | JP | R1 | 0.90 | sample.attr.geo_loc_name | Japan |
| SAMD00633985 | health_condition | other_disease | R2 | 0.75 | external.gmrepo source | phenotype: Multiple Chemical Sensitivity |
| SAMD00633985 | health_condition_detail | Multiple Chemical Sensitivity | R2 | 0.75 | external.gmrepo source | phenotype: Multiple Chemical Sensitivity |
| SAMD00633985 | location_site | Sagamihara National Hospital | R3 | 0.70 | paper.body.methods_results | Thirty consecutive Japanese female patients with MCS visiting Sagamihara National Hospital were included in the study. |
| SAMD00633985 | sex | female | R3 | 0.70 | paper.body.methods_results | Thirty consecutive Japanese female patients with MCS visiting Sagamihara National Hospital were included in the study. |
| SAMD00633985 | subject_id | SAMD00633985 | R3 | 0.75 | design.one_sample_per_subject:fulltext | due to the cross-sectional nature of the study, we cannot show a causal relationship |
Sequencing
30 runs over 30 samples · mean 1.91 Gbp per run (median 1.71 Gbp, total 57.28 Gbp; 30 runs with a base count) · layout PAIRED 30 · platform ILLUMINA 30 · models Illumina MiSeq (30) · 100% of runs with a Sandpiper profile · first public 2023-08-06
Authors (0)
No author record.
Downloads
PRJDB16312.csv.gz (1.8 KB) · parquet (71.3 KB) — all 30 samples, every field with route and confidence · PRJDB16312_determinations.csv.gz (2.8 KB) — 240 evidence rows