CBA/J mouse gut metagenome, Salmonella infection, Ohio
58 fecal metagenome samples from CBA/J mice in Ohio, USA, comparing untreated animals to those infected with Salmonella to assess gut microbiome and viral genome changes during inflammation. machine-written summary
58 samples · 58 runs · US · Age unknown · 2021 · 14.71 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 348 sample values (collection date, country, latitude, location region, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 58 sample values (location locality) · PMC10199544, PMC10653893 |
| ✓ Supplementary tables | 216 sample values (age, bmi, sex, smoking status) |
| – 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 |
Genera, mean relative abundance over 54 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 | 54 | 93% | ||||
| country | 58 | 100% | 58 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 58 | 100% | 58 | |||
| collection_date | 58 | 100% | 58 | |||
| detailed_location | 58 | 100% | ||||
| latitude | 58 | 100% | 58 | |||
| location_locality | 58 | 100% | 58 | |||
| location_region | 58 | 100% | 58 | |||
| longitude | 58 | 100% | 58 | |||
| age_at_collection_days | 54 | 93% | 54 | |||
| bmi | 54 | 93% | 54 | |||
| sex | 54 | 93% | 54 | |||
| smoking_status | 54 | 93% | 54 |
- Exposing new taxonomic variation with inflammation - a murine model-specific genome database for gut microbiome researchers. 2023 PMID 37210515 PMC10199544 own_data
- Targeted curation of the gut microbial gene content modulating human cardiovascular disease. 2023 PMID 37695138 PMC10653893 own_data
Archive description
Fecal Metagenomes
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “human gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN18867751 | age_at_collection_days | 15706 | R2 | 0.85 | paper.supp.mbio.01511-23-s0001.xlsx[Tab 3!Age] | 43 |
| SAMN18867751 | bmi | 41.8 | R2 | 0.85 | paper.supp.mbio.01511-23-s0001.xlsx[Tab 3!BMI] | 41.76774691 |
| SAMN18867751 | collection_date | 2017 | R1 | 0.90 | biosample.attribute:collection_date | 2017 |
| SAMN18867751 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA:Ohio |
| SAMN18867751 | latitude | 39.0000 | R1 | 0.90 | biosample.attribute:lat_lon | 39 N 84 W |
| SAMN18867751 | location_locality | Cincinnati | R3 | 0.70 | paper.fulltext.methods | University of Cincinnati College of Medicine |
| SAMN18867751 | location_region | Ohio | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:Ohio |
| SAMN18867751 | longitude | -84.0000 | R1 | 0.90 | biosample.attribute:lat_lon | 39 N 84 W |
| SAMN18867751 | sex | male | R2 | 0.85 | paper.supp.mbio.01511-23-s0001.xlsx[Tab 3!Sex] | M |
| SAMN18867751 | smoking_status | never | R2 | 0.85 | paper.supp.mbio.01511-23-s0001.xlsx[Tab 3!Smoker] | N |
| SAMN18867751 | subject_id | P1 | R1 | 0.85 | biosample.attribute:alias | alias: P1 |
Sequencing
58 runs over 58 samples · mean 17.62 Gbp per run (median 14.71 Gbp, total 1,021.79 Gbp; 58 runs with a base count) · layout PAIRED 58 · platform ILLUMINA 58 · models Illumina NovaSeq 6000 (58) · 93% of runs with a Sandpiper profile · first public 2021-06-27 – 2021-06-28
Authors (22)
Leleiwi I first · Rodriguez-Ramos J · Shaffer M · Sabag-Daigle A · Kokkinias K · Flynn RM · Daly RA · Kop LFM · Solden LM · Ahmer BMM · Borton MA · Wrighton KC last · Hoyt DW · Jiang R · Ellenbogen JB · Purvine S · Nicora CD · Eder EK · Wong AR · Smulian AG · Lipton MS · Krzycki JA
Downloads
PRJNA725020.csv.gz (3.0 KB) · parquet (73.3 KB) — all 58 samples, every field with route and confidence · PRJNA725020_determinations.csv.gz (5.8 KB) — 622 evidence rows