Gut metagenomes in Campylobacter infection, Michigan
70 stool samples from Michigan, USA, comparing Campylobacter-infected cases (26) and healthy family member controls (44) in a case-control design examining antibiotic resistance gene composition and diversity. machine-written summary
70 samples · 70 runs · US · Age unknown · 2022 · 1.37 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 | 560 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 · PMC10509190, PMC11109446, PMC8595376 |
| ○ 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 |
families — not resolvedhouseholds — not resolved
26 Campylobacter cases and 44 healthy family members from 16 families; per-sample family links only in a supplementary figure.
Genera, mean relative abundance over 65 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 | 70 | 100% | 70 | |||
| health_condition | 70 | 100% | 70 | |||
| subject_id | 70 | 100% | 70 | |||
| collection_date | 70 | 100% | 70 | |||
| detailed_location | 70 | 100% | ||||
| health_condition_detail | 70 | 100% | 70 | |||
| latitude | 70 | 100% | 70 | |||
| location_region | 70 | 100% | 70 | |||
| longitude | 70 | 100% | 70 |
- Comparing gut resistome composition among patients with acute Campylobacter infections and healthy family members. 2021 PMID 34785751 PMC8595376 own_data
- 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
Archive description
Metagenome sequences of human stool from patients infected with Campylobacter and healthy controls
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “human gut during enteric infection”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN15958881 | collection_date | 2012 | R1 | 0.90 | biosample.attribute:collection_date | 2012 |
| SAMN15958881 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Michigan |
| SAMN15958881 | health_condition | gi_infection_or_diarrhoea | R1 | 0.90 | biosample_attr | Campylobacteriosis |
| SAMN15958907 | health_condition | healthy_control | R1 | 0.85 | biosample.attribute:env_local_scale | Healthy |
| SAMN15958881 | health_condition_detail | Campylobacteriosis | R1 | 0.90 | sample.attr.host_disease | Campylobacteriosis |
| SAMN15958907 | health_condition_detail | Healthy | R1 | 0.85 | biosample.attribute:env_local_scale | Healthy |
| SAMN15958881 | latitude | 44.3148 | R1 | 0.90 | biosample.attribute:lat_lon | 44.3148 N 85.6024 W |
| SAMN15958881 | location_region | Michigan | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Michigan |
| SAMN15958881 | longitude | -85.6024 | R1 | 0.90 | biosample.attribute:lat_lon | 44.3148 N 85.6024 W |
| SAMN15958881 | subject_id | 27 | R1 | 0.85 | sample.attr.host_subject_id | 27 |
Sequencing
70 runs over 70 samples · mean 1.33 Gbp per run (median 1.37 Gbp, total 93.36 Gbp; 70 runs with a base count) · layout PAIRED 70 · platform ILLUMINA 70 · models Illumina HiSeq 2500 (70) · 93% of runs with a Sandpiper profile · first public 2022-09-03
Authors (17)
Hansen ZA first · Cha W · Nohomovich B · Newton DW · Lephart P · Salimnia H · Khalife W · Shade A · Rudrik JT · Manning SD last · Vasco K · Scribner KT · Zhang L · Schilmiller AL · Guzior DV · Quinn RA · Vasco KA
Downloads
PRJNA660443.csv.gz (2.6 KB) · parquet (73.2 KB) — all 70 samples, every field with route and confidence · PRJNA660443_determinations.csv.gz (4.1 KB) — 560 evidence rows