US infant/neonate gut microbiome cohort, bile acid amidates
180 longitudinal gut metagenome samples from healthy infants and neonates in the USA, studied for bacterial bile salt hydrolase activity and bile acid amidate production; cohort_longitudinal design. machine-written summary
180 samples · 180 runs · US · Infant / toddler · 2023 · 2.06 Gbp / sample · cohort Benitez 2025 USA
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,028 sample values (age, collection date, country, feeding mode, subject id, timepoint) |
| ✓ Abstract / description | 180 sample values (health condition) |
| ✓ Full text | 180 sample values (location site) · PMC11558993, PMC11761179, PMC12375414 |
| ○ 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 |
longitudinal
54 of 74 people sampled more than once (160 samples; median 3, up to 3 per person) · follow-up median 12 mo (max 12 mo) · median interval between samples 11 mo (time from age at collection). Schedule stated by the source: “Samples collected at three visits/ages: 0-4D (neonate), 1M, and 12M (infant) per subject.”.
Each row is one person (36 shown of 54); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 140 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 | 180 | 100% | ||||
| country | 180 | 100% | 180 | |||
| health_condition | 180 | 100% | 180 | |||
| subject_id | 180 | 100% | 180 | |||
| age_at_collection_days | 180 | 100% | 180 | |||
| collection_date | 180 | 100% | 180 | |||
| detailed_location | 180 | 100% | ||||
| location_site | 180 | 100% | 180 | |||
| timepoint_label | 180 | 100% | 180 | |||
| feeding_mode | 128 | 71% | 128 |
- Metal availability shapes early life microbial ecology and community succession. PMID 39440978 PMC11558993 curated
- Antibiotic exposure is associated with minimal gut microbiome perturbations in healthy term infants. PMID 39856742 PMC11761179 curated
- Amino acid competition shapes Acinetobacter baumannii gut carriage. PMID 40763731 PMC12375414 curated
Archive description
Bacteria in the gastrointestinal tract (GI) produce amino acid bile acid amidates that impact host-mediated metabolic processes however, the bacterial gene(s) responsible for their production remain unknown. Herein, we report that bile salt hydrolase (BSH) possesses dual functions in bile acid metabolism. Specifically, we identified a new role for BSH as an amine N-acyl transferase that conjugates amines to bile acids thus forming bacterial bile acid amidates (BBAAs). To characterize this amine N-acyl transferase BSH activity, we used pharmacological inhibition of BSH, heterologous expression of bsh and mutants in Escherichia coli, and a bsh knockout and complementation in Bacteroides fragilis to demonstrate that BSH generates BBAAs. We further demonstrate in a human infant cohort that BBAA production is positively correlated with the colonization of bsh-expressing bacteria. Lastly, we report that BBAAs activate host ligand-activated transcription factors including the pregnane X receptor and the aryl hydrocarbon receptor. These findings enhance our understanding of how gut bacteria, through the promiscuous actions of BSH, play a significant role in regulating the bile acid metabolic network.
How this project entered the registry
Classified as human blood / tissue / internal fluids / gut / stool shotgun DNA metagenome of infant / toddler by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.title · “Bile Acids Are Substrates”
- body site study.description · “produce amino acid bile acid amidates that”
- body site study.description · “Bacteria in the gastrointestinal tract (GI) produce”
- body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.description · “in a human infant cohort that BBAA”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN38315743 | age_at_collection_days | 30 | R1 | 0.90 | biosample_attr | 1M |
| SAMN38315743 | collection_date | 2016 | R1 | 0.85 | biosample.attribute:collection_date | 2016 |
| SAMN38315743 | country | US | R1 | 0.90 | biosample_attr | USA |
| SAMN38315743 | feeding_mode | mixed | R1 | 0.85 | biosample_attr | mixed |
| SAMN38315743 | health_condition | healthy_control | R4 | 0.50 | paper.abstract | healthy term infants |
| SAMN38315743 | location_site | Children's Hospital of Philadelphia | R3 | 0.60 | paper.fulltext.results | conducted at the Children’s Hospital of Philadelphia |
| SAMN38315743 | subject_id | s103 | R1 | 0.85 | biosample_attr | s103 |
| SAMN38315743 | timepoint_label | V02 | R1 | 0.85 | biosample.attribute:host_age | 1M |
| SAMN38315746 | timepoint_label | V07 | R1 | 0.70 | run.library_name | IgramRun3.104.2.STL.V07.12mo |
Sequencing
180 runs over 180 samples · mean 1.83 Gbp per run (median 2.06 Gbp, total 329.09 Gbp; 180 runs with a base count) · layout PAIRED 180 · platform ILLUMINA 180 · models Illumina HiSeq 2500 (180) · 78% of runs with a Sandpiper profile · first public 2023-11-19
Authors (59)
Rimal B first · Collins SL · Tanes CE · Rocha ER · Granda MA · Solanki S · Hoque NJ · Gentry EC · Koo I · Reilly ER · Hao F · Paudel D · Singh V · Yan T · Kim MS · Bittinger K · Zackular JP · Krausz KW · Desai D · Amin S · Coleman JP · Shah YM · Bisanz JE · Gonzalez FJ · Vanden Heuvel JP · Wu GD · Zemel BS · Dorrestein PC · Weinert EE · Patterson AD last · Soto Ocaña J first · Friedman ES · Keenan O · Bayard NU · Ford E · Tanes C · Munneke MJ · Beavers WN · Skaar EP · Benitez AJ first · Gerber JS · DeRusso PA · Kelly A · Li H · Elovitz MA · Zemel B · Ren X first · Clark RM · Bansah DA · Varner EN · Tiffany CR · Jaswal K · Geary JH · Todd OA · Winkelman JD · Jarrett RN · DePas WH · Behnsen J · Palmer LD last
Downloads
PRJNA1042647.csv.gz (6.4 KB) · parquet (78.2 KB) — all 180 samples, every field with route and confidence · PRJNA1042647_determinations.csv.gz (8.2 KB) — 1,388 evidence rows