Gut microbiome and BCG vaccine trained immunity, Netherlands
323 stool/blood samples from healthy adults (and elderly) in the Netherlands, in an intervention study examining gut microbiome influence on BCG vaccine-induced specific and trained immune responses. machine-written summary
323 samples · 323 runs · NL · Adult · 2021 · 4.03 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,286 sample values (age, country, sex, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 646 sample values (health condition, health condition detail) · PMC13427514, PMC8456614 |
| ○ 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 |
intervention — arms not resolved
Vaccination as the study intervention design single_arm_before_after · population healthy_control · BCG vaccination with pre/post blood and stool sampling
“stool and blood were collected from 321 healthy adults before BCG vaccination” — bioproject.description (study level; per-sample arms are in the intervention column below)
Genera, mean relative abundance over 298 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 | 323 | 100% | ||||
| country | 323 | 100% | 323 | |||
| health_condition | 323 | 100% | 323 | |||
| subject_id | 0 | 0% | ||||
| health_condition_detail | 323 | 100% | 323 | |||
| timepoint_label | 323 | 100% | 323 | |||
| age_at_collection_days | 320 | 99% | 320 | |||
| sex | 320 | 99% | 320 |
- The influence of the gut microbiome on BCG-induced trained immunity. 2021 PMID 34551799 PMC8456614 own_data
- Investigating the role of baseline gut Akkermansia muciniphila and its co-metabolite palmitoleic acid in BCG vaccine efficacy: a preclinical study. 2026 PMID 42492179 PMC13427514 own_data
Archive description
The bacillus Calmette-Guerin (BCG) vaccine protects against tuberculosis and heterologous infections, but elicits high interindividual variation in specific and nonspecific (trained) immune responses. As the gut microbiome might mediate this variability, stool and blood were collected from 321 healthy adults before BCG vaccination, followed by blood sampling two weeks and three months afterwards. Metagenomics based on de novo genome assemble revealed 43 taxa associated with increased cytokine production upon ex vivo blood restimulation by Mycobacterium tuberculosis and Staphylococcus aureus. Trained responses negatively correlated with Roseburia, while specific responses associated positively with Ruminococcus and Eggerthella Ienta. The immunomodulatory taxa identified also had the strongest effects on circulating metaboloties, with Roseburia predominantly affecting phenylalanine metabolism. This was corroborated by abundances of relevant enzymes, suggesting alternate phenylalanine metabolism modules are activated in a Roseburia species-dependent manner. These findings reveal microbes and their products that may alter BCG-induced specific and trained immune responses.
How this project entered the registry
Classified as human gut / stool / blood / tissue / internal fluids shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “Influence of the gut microbiome on BCG-induced”
- body site study.description · “responses. As the gut microbiome might mediate”
- body site study.description · “variability, stool and blood were collected from”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- life stage study.description · “from 321 healthy adults before BCG vaccination,”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN17111868 | age_at_collection_days | 8400.8 | R1 | 0.70 | sample.attr.age | 23 |
| SAMN17111868 | country | NL | R1 | 0.90 | sample.attr.geo_loc_name | Netherlands: Europe |
| SAMN17111868 | health_condition | healthy_control | R3 | 0.70 | paper.fulltext.methods | 321 healthy subjects following vaccination with BCG |
| SAMN17111868 | health_condition_detail | healthy subjects following vaccination with BCG | R3 | 0.70 | paper.fulltext.methods | 321 healthy subjects following vaccination with BCG |
| SAMN17111868 | sex | female | R1 | 0.90 | sample.attr.sex | female |
| SAMN17111868 | timepoint_label | V1 | R1 | 0.70 | sample.name_rule:TITLE | TITLE: 001_V1 |
Sequencing
323 runs over 323 samples · mean 4.10 Gbp per run (median 4.03 Gbp, total 1,324.68 Gbp; 323 runs with a base count) · layout PAIRED 323 · platform ILLUMINA 323 · models Illumina NovaSeq 6000 (323) · 92% of runs with a Sandpiper profile · first public 2021-09-22 – 2021-09-23
Authors (41)
Stražar M first · Mourits VP · Koeken VACM · de Bree LCJ · Moorlag SJCFM · Joosten LAB · van Crevel R · Vlamakis H · Netea MG · Xavier RJ last · Argentini C first · Lugli GA · Tarracchini C · Fontana F · Mancabelli L · Viappiani A · Anzalone R · Angelini L · Alessandri G · Longhi G · Bianchi MG · Taurino G · Bussolati O · Milani C · van Sinderen D · Turroni F · Ventura M last · Chen D first · Chen L · Chen C · Yan Y · Wu X · Yuan P · Long X · Zou Y · Lin J · Xu JF · Pi J · Zeng G · Lu Y · Ge Z last
Downloads
PRJNA685797.csv.gz (9.0 KB) · parquet (82.5 KB) — all 323 samples, every field with route and confidence · PRJNA685797_determinations.csv.gz (11.2 KB) — 1,932 evidence rows