Probiotic engraftment in healthy adults, Nebraska, USA
65 fecal samples from healthy adults in Lincoln, Nebraska, USA, collected before and after oral administration of the probiotic strain Bifidobacterium longum AH1206, in an intervention study of gut colonization. machine-written summary
65 samples · 65 runs · US · Adult · 2016 · 3.10 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 889 sample values (age, bmi, collection date, country, diet, diet detail, intervention, latitude) |
| ✓ Abstract / description | 130 sample values (health condition, health condition detail) |
| ○ Full text | read; no usable statement or table · PMC10349097, PMC10942782 |
| ○ 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
Probiotic (live microorganisms; single strain or mixture) design single_arm_before_after · population healthy_control · Oral administration of Bifidobacterium longum AH1206 probiotic strain
“before and after consumption of AH1206” — study.title (study level; per-sample arms are in the intervention column below)
longitudinal
22 of 22 people sampled more than once (65 samples; median 3, up to 3 per person) · follow-up median 7 mo (max 8 mo) · median interval between samples 13 d (time from collection dates). Schedule stated by the source: “baseline (pre-treatment), treatment (during AH1206 consumption), persistence (~200 days after interruption of consumption)” (time origin: intervention_start); stated follow-up 7 mo.
Each row is one person (22 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 60 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 | 65 | 100% | ||||
| country | 65 | 100% | 65 | |||
| health_condition | 65 | 100% | 65 | |||
| subject_id | 65 | 100% | 65 | |||
| age_at_collection_days | 65 | 100% | 65 | |||
| bmi | 65 | 100% | 65 | |||
| collection_date | 65 | 100% | 65 | |||
| detailed_location | 65 | 100% | ||||
| diet | 65 | 100% | 65 | |||
| diet_detail | 65 | 100% | 65 | |||
| health_condition_detail | 65 | 100% | 65 | |||
| latitude | 65 | 100% | 65 | |||
| location_locality | 65 | 100% | 65 | |||
| location_region | 65 | 100% | 65 | |||
| longitude | 65 | 100% | 65 | |||
| sex | 65 | 100% | 65 | |||
| timepoint_label | 65 | 100% | 65 | |||
| intervention | 44 | 68% | 44 |
- Metabolic model-based ecological modeling for probiotic design. 2024 PMID 38380900 PMC10942782 own_data
- Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner. 2021 PMID 34226711 PMC8318886 unsure
- Probiotic consumption influences universal adaptive mutations in indigenous human and mouse gut microbiota. 2021 PMID 34663913 PMC8523657 unsure
- Genetic strategies for sex-biased persistence of gut microbes across human life. 2023 PMID 37452041 PMC10349097 unsure
- Plasmids in the human gut reveal neutral dispersal and recombination that is overpowered by inflammatory diseases. 2024 PMID 38605009 PMC11009399 unsure
2 more
- Integrating comparative genomics and risk classification by assessing virulence, antimicrobial resistance, and plasmid spread in microbial communities with gSpreadComp. 2025 PMID 40569694 PMC12199706
- Plasmid dispersal and recombination across human gut microbiomes is neutral, but overpowered by inflammatory diseases 2023
Archive description
Live bacteria have been used for decades in an attempt to modulate the human gut microbiota, but their colonization is mostly transient, and a conceptual understanding of the ecological role of exogenous microbes in gut ecosystems is lacking. Here we show that Bifidobacterium longum AH1206 stably persists in the gut of one third of human individuals for at least six months after being orally administered without causing gastrointestinal symptoms or impacting the composition of the resident gut microbiota. Engraftment of AH1206 was associated with low abundance of B. longum and specific carbohydrate utilization genes of this species in the pre-treatment microbiome. This pointed to inter-individual differences in the availability of resources that constitute a niche opportunity for colonization. The findings suggest that bacterial species and functional genes absent in the gut microbiome of individual humans can be reestablished, providing opportunities for precision microbiome reconstitution and a personalization of such strategies.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host study.title · “Human fecal microbiome before and after consumption”
- body site study.title · “Human fecal microbiome”
- life stage sample.attr.host_age · “24 (n=65/65)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN05194690 | age_at_collection_days | 13878.5 | R1 | 0.85 | sample.attr.host_age | 38 |
| SAMN05194690 | bmi | 20.2 | R1 | 0.90 | sample.attr.host_body_mass_index | 20.2 |
| SAMN05194690 | collection_date | 2012-10-23 | R1 | 0.90 | biosample.attribute:collection_date | 2012-10-23 |
| SAMN05194690 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Lincoln, Nebraska |
| SAMN05194690 | diet | omnivore | R1 | 0.90 | biosample.attribute:host_diet | Omnivore |
| SAMN05194690 | diet_detail | Omnivore | R1 | 0.90 | biosample.attribute:host_diet | Omnivore |
| SAMN05194690 | health_condition | healthy_control | R4 | 0.45 | study.description | orally administered without causing gastrointestinal symptoms |
| SAMN05194690 | health_condition_detail | healthy volunteers receiving probiotic intervention | R4 | 0.45 | study.description | orally administered without causing gastrointestinal symptoms |
| SAMN05194690 | intervention | no_intervention | R1 | 0.70 | sample.name_rule:alias | baseline |
| SAMN05194690 | latitude | 40.8290 | R1 | 0.90 | biosample.attribute:lat_lon | 40.829 N 96.667 W |
| SAMN05194690 | location_locality | Lincoln | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Lincoln, Nebraska |
| SAMN05194690 | location_region | Nebraska | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Lincoln, Nebraska |
| SAMN05194690 | longitude | -96.6670 | R1 | 0.90 | biosample.attribute:lat_lon | 40.829 N 96.667 W |
| SAMN05194690 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
| SAMN05194690 | subject_id | A | R1 | 0.70 | sample.name_rule:alias | A |
| SAMN05194690 | timepoint_label | baseline | R1 | 0.70 | sample.name_rule:alias | baseline |
Sequencing
65 runs over 65 samples · mean 3.11 Gbp per run (median 3.10 Gbp, total 202.42 Gbp; 65 runs with a base count) · layout PAIRED 65 · platform ILLUMINA 65 · models Illumina HiSeq 2500 (65) · 92% of runs with a Sandpiper profile · first public 2016-07-20 – 2016-08-08
Authors (41)
Montassier E first · Valdés-Mas R · Batard E · Zmora N · Dori-Bachash M · Suez J · Elinav E last · Brunner JD first · Chia N 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 · Zorea A first · Pellow D · Levin L · Pilosof S · Friedman J · Shamir R · Mizrahi I last · Kasmanas JC first · Magnúsdóttir S · Zhang J · Smalla K · Schloter M · Stadler PF · de Leon Ferreira de Carvalho ACP · Rocha U last
Downloads
PRJNA324129.csv.gz (3.0 KB) · parquet (75.0 KB) — all 65 samples, every field with route and confidence · PRJNA324129_determinations.csv.gz (8.1 KB) — 1,019 evidence rows