Early-life gut microbiota and colonisation resistance
772 samples studied to understand how bifidobacteria colonise the infant gut, modulate colonisation resistance, and how antibiotic-induced disturbances affect this community and pathogen protection. Country, age, and health details are not specified. machine-written summary
772 samples · 168 runs · Infant / toddler · 2018 · 1.02 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 467 sample values (health condition, health condition detail, sex, 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 |
intervention — arms not resolved
design observational_with_procedure
longitudinal — not resolved
3 of 102 people sampled more than once (12 samples; median 4, up to 5 per person).
Genera, mean relative abundance over 151 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 | 0 | 0% | ||||
| health_condition | 96 | 12% | 96 | |||
| subject_id | 164 | 21% | 164 | |||
| health_condition_detail | 120 | 16% | 120 | |||
| sex | 48 | 6% | 48 | |||
| timepoint_label | 39 | 5% | 39 |
Archive description
The aim is to understand how (i) bifidobacteria colonise the gut and (ii) subsequently modulate critical colonisation resistance, and to understand how (iii) early life antibiotic-induced disturbances alter this microbial community, ultimately leading to a breakdown in pathogen protection. Another key goal is to (iv) identify bifidobacterial communities that can restore a disturbed early life microbiota back into one able to control gut infection. These data are part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler by sonnet_x2 with confidence 0.57. Assay shotgun_dna.
- host run.scientific_name · “gut metagenome(92)”
- body site run.scientific_name · “feces metagenome(76)”
- life stage study.title · “Role_of_early_life_gut_microbiota”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA44473918 | health_condition | preterm_nicu | R1 | 0.85 | biosample.attribute:sample_description | bacterial DNA from preterm faeces |
| SAMEA44473918 | health_condition_detail | bacterial DNA from preterm faeces | R1 | 0.85 | biosample.attribute:sample_description | bacterial DNA from preterm faeces |
| SAMEA5867038 | health_condition_detail | human faecal microbiota | R1 | 0.90 | biosample.attribute:arrayexpress_phenotype | arrayexpress_phenotype: human faecal microbiota |
| SAMEA104703327 | sex | female | R1 | 0.90 | biosample_attr | Female |
| SAMEA3890332 | sex | female | R1 | 0.90 | biosample.attribute:arrayexpress_sex | arrayexpress_sex: female |
| SAMEA103926772 | subject_id | 3258STDY6719825 | R1 | 0.85 | biosample_attr | 3258STDY6719825 |
| SAMEA5869431 | subject_id | P29 | R1 | 0.70 | sample.name_rule:sample_title | P29F |
| SAMEA104054935 | timepoint_label | D6 | R1 | 0.70 | run.library_name | DN483663W:D6 |
Sequencing
1,067 runs over 772 samples · mean 0.87 Gbp per run (median 90.5 Mbp, total 927.49 Gbp; 1,067 runs with a base count) · layout PAIRED 1,067 · platform ILLUMINA 1,067 · models Illumina MiSeq (662), Illumina HiSeq 2500 (323), Illumina HiSeq 2000 (82) · 14% of runs with a Sandpiper profile · first public 2015-01-27 – 2020-04-14
Authors (0)
No author record.
Help complete this project
4 of the 4 core fields are below 50% coverage: age_category, country, health_condition, subject_id. Share metadata
Downloads
PRJEB6921.csv.gz (19.5 KB) · parquet (102.4 KB) — all 772 samples, every field with route and confidence · PRJEB6921_determinations.csv.gz (4.8 KB) — 467 evidence rows