Gut carriage of Acinetobacter baumannii in US infants, diet study
45 fecal samples from healthy infants in the USA, examining diet (formula vs. other feeding) effects on gut carriage of Acinetobacter baumannii. machine-written summary
45 samples · 45 runs · US · Infant / toddler · 2024 · 1.97 Gbp / sample · cohort Glucuronidation metabolomic fingerprinting to map
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 360 sample values (age, collection date, country, diet, latitude, location region, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 180 sample values (antibiotic exposure, health condition, health condition detail, location site) · PMC12375414, PMC13381908 |
| ○ 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
Controlled / prescribed diet or feeding regimen design single_arm_before_after · population gi_infection_or_diarrhoea · Dietary ornithine, MSG, or histidine supplementation in mice colonized with A. baumannii
“Supplemental dietary ornithine promotes long-term fecal shedding” — abstract:40763731 (study level; per-sample arms are in the intervention column below)
Genera, mean relative abundance over 38 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 | 45 | 100% | ||||
| country | 45 | 100% | 45 | |||
| health_condition | 45 | 100% | 45 | |||
| subject_id | 45 | 100% | 45 | |||
| age_at_collection_days | 45 | 100% | 45 | |||
| antibiotic_exposure | 45 | 100% | 45 | |||
| collection_date | 45 | 100% | 45 | |||
| detailed_location | 45 | 100% | ||||
| diet | 45 | 100% | 45 | |||
| health_condition_detail | 45 | 100% | 45 | |||
| latitude | 45 | 100% | 45 | |||
| location_region | 45 | 100% | 45 | |||
| location_site | 45 | 100% | 45 | |||
| longitude | 45 | 100% | 45 |
- Amino acid competition shapes Acinetobacter baumannii gut carriage. 2025 PMID 40763731 PMC12375414 own_data
- Glucuronidation metabolomic fingerprinting to map host-microbe metabolism. 2026 PMID 42161945 PMC13381908 unsure
Archive description
Antimicrobial resistant (AMR) infections are a critical threat to human health. Asymptomatic colonization is often critical for persistence of AMR pathogens. Gut colonization by the AMR priority pathogen Acinetobacter baumannii is associated with increased risk of clinical infection. Ecological factors shaping A. baumannii colonization and mechanisms of competition with the resident microbiota remain unclear. Here we show that A. baumannii encodes a second ast operon to utilize ornithine, a non-preferred carbon source, to compete with the resident microbiota and persist in the gut. Supplemental dietary ornithine promotes long-term fecal shedding of A. baumannii. By contrast, supplementation of a preferred carbon source-monosodium glutamate (MSG)-abolishes the requirement for A. baumannii ornithine catabolism. We report evidence for diet promoting asymptomatic A. baumannii gut colonization in humans. Together, these results highlight that evolution of ornithine catabolism allows A. baumannii to compete with the microbiota in the gut, a reservoir for pathogen spread.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler by sonnet_x2 with confidence 0.68. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.description · “evidence for diet promoting asymptomatic A. baumannii gut colonization in humans”
- body site run.scientific_name · “human gut metagenome”
- life stage sample.attr.host_age · “1M (n=45/45)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN44297978 | age_at_collection_days | 30.0 | R1 | 0.90 | sample.attr.host_age | 1M |
| SAMN44297978 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | infants who had never received antibiotics |
| SAMN44297978 | collection_date | 2016 | R1 | 0.90 | biosample.attribute:collection_date | 2016 |
| SAMN44297978 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN44297978 | diet | exclusive_breast_milk | R1 | 0.85 | biosample.attribute:feeding_type | breastmilk |
| SAMN44297978 | health_condition | healthy_control | R3 | 0.70 | paper.fulltext.methods | had no history of health problems |
| SAMN44297978 | health_condition_detail | no history of health problems | R3 | 0.70 | paper.fulltext.methods | had no history of health problems |
| SAMN44297978 | latitude | 39.9560 | R1 | 0.90 | biosample.attribute:lat_lon | 39.956 N 75.193 W |
| SAMN44297978 | location_region | Pennsylvania | R1 | 0.60 | biosample.attribute:lat_lon | 39.956 N 75.193 W |
| SAMN44297978 | location_site | Children's Hospital of Philadelphia | R3 | 0.70 | paper.fulltext.methods | Children's Hospital of Philadelphia as part of the Infant Growth |
| SAMN44297978 | longitude | -75.1930 | R1 | 0.90 | biosample.attribute:lat_lon | 39.956 N 75.193 W |
| SAMN44297978 | subject_id | s314 | R1 | 0.85 | sample.attr.host_subject_id | s314 |
Sequencing
45 runs over 45 samples · mean 1.91 Gbp per run (median 1.97 Gbp, total 85.81 Gbp; 45 runs with a base count) · layout PAIRED 45 · platform ILLUMINA 45 · models Illumina HiSeq 2500 (45) · 84% of runs with a Sandpiper profile · first public 2024-10-20
Authors (37)
Ren X first · Clark RM · Bansah DA · Varner EN · Tiffany CR · Jaswal K · Geary JH · Todd OA · Winkelman JD · Friedman ES · Jarrett RN · Zemel BS · Wu GD · Zackular JP · DePas WH · Behnsen J · Palmer LD last · Boyle NR first · Sekela JJ · Wang M · Mannochio-Russo H · Pyo JJ · Kim MS · Tian S · Koo I · Tanes C · Anitha M · Tian Y · Morgan EW · Murray IA · Bittinger K · Lewis JD · Perdew GH · Dorrestein PC · Bisanz JE · Redinbo MR · Patterson AD last
Downloads
PRJNA1173239.csv.gz (2.3 KB) · parquet (72.8 KB) — all 45 samples, every field with route and confidence · PRJNA1173239_determinations.csv.gz (4.1 KB) — 540 evidence rows