Fecal & oropharyngeal microbiota, infant CF beta-lactam use
148 fecal and oropharyngeal samples from infants with cystic fibrosis (14 treated with beta-lactam antibiotics, 5 untreated controls), studied longitudinally to compare respiratory versus fecal microbiome effects of antibiotic treatment. machine-written summary
148 samples · 148 runs · Infant / toddler · 2025 · 2.95 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 379 sample values (antibiotic exposure, subject id, timepoint) |
| ✓ Abstract / description | 148 sample values (health condition) |
| ○ Full text | read; no usable statement or table · PMC11881217 |
| ✓ Supplementary tables | 200 sample values (age, antibiotic exposure) |
| – 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
Antibiotic given as the study intervention (incl. eradication therapy design observational_with_procedure · population other_disease · Beta-lactam antibiotics for respiratory exacerbations; sampled on vs off vs never treated
“β-lactam therapy, and from 5 IWCF” — abstract:40042126 (study level; per-sample arms are in the intervention column below)
longitudinal
14 of 14 people sampled more than once (74 samples; median 5, up to 10 per person) · follow-up median 4 mo (max 8 mo) · median interval between samples 29 d (time from age at collection).
Each row is one person (13 shown of 14); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 72 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 | 140 | 95% | ||||
| country | 0 | 0% | ||||
| health_condition | 148 | 100% | 148 | |||
| subject_id | 148 | 100% | 148 | |||
| timepoint_label | 148 | 100% | 148 | |||
| antibiotic_exposure | 143 | 97% | 83 | 60 | ||
| age_at_collection_days | 140 | 95% | 140 |
- Effects of Therapeutic Antibiotic Exposure on the Oropharyngeal and Fecal Microbiota in Infants With Cystic Fibrosis. PMID 40042126 PMC11881217 curated
Archive description
Cystic fibrosis (CF) is a multiorgan disease caused by mutations in the CF transmembrane conductance regulator (CFTR) that alter the transport of fluid and ions across cell membranes. Complications from CF, including lung infections, begin in early in life, and infants with cystic fibrosis frequently receive systemic antibiotics for respiratory symptoms. Systemic antibiotic treatments can impact all colonizing and infecting microbes inhabiting patients, regardless of the intended target organism(s). We studied the simultaneous effects on the respiratory and fecal microbiomes of beta-lactam antibiotics administered for respiratory symptoms in infants with CF to compare the magnitude and duration of intended (respiratory) and unintended (fecal) antimicrobial action. We performed shotgun metagenomic sequencing and qPCR analysis of oropharyngeal (OP) and fecal samples from 14 infants with CF off and on beta-lactam therapy, and from 5 untreated control infants with CF. We found that beta-lactam antibiotic treatments for CF respiratory exacerbations were followed by a longer-lasting change in fecal than OP microbiota. These changes led to alterations in known antibiotic resistance gene complements in both sample types that could not be explained by selection for canonical beta-lactam resistance genes, limiting the ability to predict off-target effects with pre-treatment testing and potentially impacting the effects of subsequent antibiotic treatments.
How this project entered the registry
Classified as human gut / stool / lower respiratory 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 · “Fecal and oropharyngeal microbiota”
- body site study.description · “the respiratory and fecal microbiomes of beta-lactam”
- body site study.description · “from CF, including lung infections, begin in”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “oropharyngeal microbiota from infants with cystic fibrosis”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN37384032 | age_at_collection_days | 144.0 | R2 | 0.80 | paper.supp.PPUL-60-0-s002.docx[table2!Age at collection (days)] | Age at collection (days): 144 |
| SAMN37384034 | antibiotic_exposure | yes | R1 | 0.70 | sample.name_rule:library_names | I.EMB.001.OP.On.01 |
| SAMN37384032 | antibiotic_exposure | yes | R2 | 0.80 | paper.supp.PPUL-60-0-s002.docx[table2!Sample group] | Sample group: Off antibiotics |
| SAMN37384032 | health_condition | other_disease | R4 | 0.45 | study.description | infants with cystic fibrosis frequently receive systemic antibiotics |
| SAMN37384032 | subject_id | C.EMB.001 | R1 | 0.70 | sample.name_rule:library_names | C.EMB.001.OP.Off.01 |
| SAMN37384032 | timepoint_label | Off 01 | R1 | 0.70 | sample.name_rule:library_names | C.EMB.001.OP.Off.01 |
Sequencing
148 runs over 148 samples · mean 3.46 Gbp per run (median 2.95 Gbp, total 511.63 Gbp; 148 runs with a base count) · layout PAIRED 148 · platform ILLUMINA 148 · models NextSeq 500 (148) · 97% of runs with a Sandpiper profile · first public 2025-05-23
Authors (14)
Hayden HS first · Nelson MT · Ross SE · Verster AJ · Bouzek DC · Eng A · Waalkes A · Penewit K · Kopp BT · Siracusa C · Rock MJ · Salipante SJ · Hoffman LR · Sanders DB last
Downloads
PRJNA1015704.csv.gz (5.6 KB) · parquet (76.6 KB) — all 148 samples, every field with route and confidence · PRJNA1015704_determinations.csv.gz (7.4 KB) — 727 evidence rows