Gut resistome prediction, MetaHIT, France/Netherlands/Spain
114 samples from a cross-sectional study across France, Netherlands, and Spain, used to characterize the intestinal antibiotic resistome via a novel 3D structure-based prediction method. machine-written summary
114 samples · 1,077 runs · FR, NL, ES · Age unknown · 2018 · 3.14 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 333 sample values (antibiotic exposure, country, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal — not resolved
26 of 50 people sampled more than once (52 samples; median 2, up to 2 per person).
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 114 | 100% | 114 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 76 | 67% | 76 | |||
| antibiotic_exposure | 93 | 82% | 93 | |||
| timepoint_label | 50 | 44% | 50 |
- Prediction of the intestinal resistome by a three-dimensional structure-based method. 2019 PMID 30478291 own_data
Archive description
The intestinal microbiota is considered to be a major reservoir of antibiotic resistance determinants (ARDs) that could potentially be transferred to bacterial pathogens. Yet, this question remains hypothetical because of the difficulty to identify ARDs from intestinal bacteria. Here, we developed and validated a new annotation method (called pairwise comparative modelling, PCM) based on homology modelling in order to characterize the Human intestinal resistome. We were able to predict 6,095 ARDs in a 3.9 million protein catalogue from the Human intestinal microbiota. We found that predicted ARDs (pdARDs) were distantly related to known ARDs (mean amino-acid identity 29.8%) and mostly (95.6%) located on the bacterial chromosome. Still, genes associated with mobility were found in the neighbourhood of 7.9% (484/6,095) of pdARDs. According to the composition of their resistome, we were able to cluster subjects from the MetaHIT cohort (n=663) into 6 “resistotypes”. Finally, we found that the relative abundance of pdARDs was positively associated with gene richness, but not when subjects were exposed to antibiotics. Altogether, our results support that most ARDs in the intestinal microbiota shall be considered as intrinsic genes of commensal microbiota with a low risk of transfer to bacterial pathogens.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.72. Assay shotgun_dna.
- host study.description · “Human intestinal resistome”
- body site run.scientific_name · “human gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA4799869 | antibiotic_exposure | yes | R1 | 0.70 | biosample_attr | Hospitalization |
| SAMEA4799856 | country | FR | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | France |
| SAMEA4799856 | subject_id | Evo_Bichat_1_001 | R1 | 0.70 | sample.name_rule:alias | Evo_Bichat_1_001_T0 |
| SAMEA4799856 | timepoint_label | T0 | R1 | 0.70 | sample.name_rule:alias | Evo_Bichat_1_001_T0 |
Sequencing
1,077 runs over 114 samples · mean 0.35 Gbp per run (median 0.22 Gbp, total 374.09 Gbp; 1,077 runs with a base count) · layout SINGLE 1,077 · platform ABI_SOLID 1,077 · models AB 5500xl Genetic Analyzer (1,077) · 0% of runs with a Sandpiper profile · first public 2018-07-27
Authors (36)
Ruppé E first · Ghozlane A · Tap J · Pons N · Alvarez AS · Maziers N · Cuesta T · Hernando-Amado S · Clares I · Martínez JL · Coque TM · Baquero F · Lanza VF · Máiz L · Goulenok T · de Lastours V · Amor N · Fantin B · Wieder I · Andremont A · van Schaik W · Rogers M · Zhang X · Willems RJL · de Brevern AG · Batto JM · Blottière HM · Léonard P · Léjard V · Letur A · Levenez F · Weiszer K · Haimet F · Doré J · Kennedy SP · Ehrlich SD last
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata
Downloads
PRJEB27799.csv.gz (3.7 KB) · parquet (73.7 KB) — all 114 samples, every field with route and confidence · PRJEB27799_determinations.csv.gz (2.9 KB) — 333 evidence rows