Gut metagenome in enteric infection, Michigan
151 samples from Michigan, USA, profiling the human gut metagenome during and after enteric infection; curated health conditions include healthy controls (55) and sepsis or infection (36). machine-written summary
151 samples · 151 runs · US · Infant / toddler · 2023 · 1.44 Gbp / sample · cohort Recovery of the gut microbiome following enteric i
One study deposited as 2 BioProjects (221 catalog samples together): PRJNA660443 · PRJNA862908 · show together
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 755 sample values (collection date, country, health condition, health condition detail, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 151 sample values (location region) · PMC10509190, PMC11109446 |
| ✓ Supplementary tables | 283 sample values (lifestyle, lifestyle detail, timepoint) |
| – 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 |
longitudinal — not resolved
Schedule stated by the source: “Paired stool samples collected during enteric infection (case) and after recovery (follow-up) from the same patients.” (time origin: infection onset).
Genera, mean relative abundance over 144 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 | 151 | 100% | 151 | |||
| health_condition | 151 | 100% | 151 | |||
| subject_id | 151 | 100% | 151 | |||
| collection_date | 151 | 100% | 151 | |||
| detailed_location | 151 | 100% | ||||
| health_condition_detail | 151 | 100% | 151 | |||
| location_region | 151 | 100% | 151 | |||
| timepoint_label | 95 | 63% | 95 | |||
| lifestyle | 94 | 62% | 94 | |||
| lifestyle_detail | 94 | 62% | 94 |
- Recovery of the gut microbiome following enteric infection and persistence of antimicrobial resistance genes in specific microbial hosts. 2023 PMID 37726374 PMC10509190 own_data
- Shifts in the functional capacity and metabolite composition of the gut microbiome during recovery from enteric infection. 2024 PMID 38779558 PMC11109446 own_data
- Recovery of the gut microbiome following enteric infection and persistence of antimicrobial resistance genes in specific microbial hosts 2023 own_data
Archive description
This study sought to characterize the human gut metagenome during enteric infection and after recovery.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.title · “Human gut metagenome during and”
- body site study.description · “characterize the human gut metagenome during enteric”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN29999523 | collection_date | 2011 | R1 | 0.85 | biosample.attribute:collection_date | 2011 |
| SAMN29999523 | country | US | R1 | 0.90 | biosample_attr | USA: Michigan |
| SAMN29999523 | health_condition | sepsis_or_infection | R1 | 0.90 | sample.attr.host_disease | host_disease=Salmonellosis |
| SAMN29999529 | health_condition | gi_infection_or_diarrhoea | R1 | 0.85 | biosample.attribute:host_phenotype | Recovered |
| SAMN29999523 | health_condition_detail | Infected | R1 | 0.90 | biosample.attribute:host_phenotype | host_phenotype: Infected |
| SAMN29999523 | lifestyle | rural_non_industrialized | R2 | 0.80 | paper.supp.Table_1.xlsx[Sheet1!Residence type] | ER0003: Rural |
| SAMN29999523 | lifestyle_detail | Rural | R2 | 0.80 | paper.supp.Table_1.xlsx[Sheet1!Residence type] | ER0003: Rural |
| SAMN29999523 | location_region | Michigan | R3 | 0.70 | paper.body.fulltext | We conducted a longitudinal case-control study in Michigan |
| SAMN29999523 | subject_id | 97 | R1 | 0.85 | biosample_attr | 97 |
| SAMN29999523 | timepoint_label | Case | R2 | 0.80 | paper.supp.Table_1.xlsx[Sheet1!Health Status] | ER0003: Case |
Sequencing
151 runs over 151 samples · mean 1.44 Gbp per run (median 1.44 Gbp, total 217.73 Gbp; 151 runs with a base count) · layout PAIRED 151 · platform ILLUMINA 151 · models Illumina HiSeq 2500 (151) · 95% of runs with a Sandpiper profile · first public 2023-08-27
Authors (0)
No author record.
Downloads
PRJNA862908.csv.gz (5.2 KB) · parquet (77.8 KB) — all 151 samples, every field with route and confidence · PRJNA862908_determinations.csv.gz (9.9 KB) — 1,189 evidence rows