Antibiotic Impact on Gut Microbiome in Malawian Adults
Longitudinal shotgun metagenomic sequencing of 450 stool and rectal-swab samples from 163 adults in Blantyre, Malawi, profiling gut microbiome and resistome changes before, during, and after antimicrobial treatment. machine-written summary
450 samples · 453 runs · MW · Adult · 2025 · 11.43 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,350 sample values (collection date, country, subject id) |
| ✓ Abstract / description | 450 sample values (location locality) |
| ○ Full text | read; no usable statement or table · PMC12847964 |
| ○ 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
163 of 163 people sampled more than once (450 samples; median 3, up to 5 per person) · follow-up median 54 d (max 7 mo) · median interval between samples 28 d (time from collection dates). Schedule stated by the source: “Baseline (visit 0, within 24h of admission) then visits at days 7, 28, 90, 180 (community arm omits days 7 and 90)”; stated follow-up 6 mo.
Each row is one person (36 shown of 163); dots are samples at days since that person's first sample.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 450 | 100% | ||||
| country | 450 | 100% | 450 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 450 | 100% | 450 | |||
| collection_date | 450 | 100% | 450 | |||
| detailed_location | 450 | 100% | ||||
| location_locality | 450 | 100% | 450 |
- Quantifying the bystander effect of antimicrobial use on the gut microbiome and resistome in Malawian adults. 2025 PMID 41423629 PMC12847964 own_data
Archive description
Antibiotic treatment for sepsis has an unintended yet crucial consequence: it exerts a bystander effect on the microbiome changing its bacterial composition and resistome. Antimicrobial stewardship aims, in part, to minimise this effect to prevent development of subsequent drug-resistant infection, but data evaluating and quantifying these changes are largely lacking, especially in low-income settings which are disproportionately affected by antimicrobial resistance. Such data are critical to creating evidence-based stewardship protocols. We address this data gap in Blantyre, Malawi. We used longitudinal sampling of human stool and metagenomic deep sequencing to describe microbiome composition and resistome pre-, during- and post-antimicrobial exposure. We developed Bayesian regression models to link these changes to individual antimicrobial agents. We find that ceftriaxone, in particular, exerts strong off-target effects, both increasing abundance of Enterobacterales, and the prevalence of macrolide and aminoglycoside resistance genes. Simulation from the fitted models allows exploration of different stewardship strategies, and can inform practice in Malawi and elsewhere.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by curator_audit with confidence 0.60. Assay shotgun_dna.
- host runs.scientific_name · “human gut metagenome (453)”
- host papers[0].abstract · “longitudinal sampling of human stool and metagenomic deep sequencing”
- body site runs.scientific_name · “human gut metagenome (453)”
- body site papers[0].abstract · “longitudinal sampling of human stool and metagenomic deep sequencing”
- life stage study.title · “gut microbiome in Malawian adults”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA117808963 | collection_date | 2017-07-14 | R1 | 0.85 | biosample.attribute:collection_date | collection_date: 2017-07-14 |
| SAMEA117808963 | country | MW | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Malawi |
| SAMEA117808963 | location_locality | Blantyre | R4 | 0.45 | ena.study_description | We address this data gap in Blantyre, Malawi |
| SAMEA117808963 | subject_id | DAS1078Y | R1 | 0.70 | sample.name_rule:title | attr:title: DAS1078Y |
Sequencing
453 runs over 450 samples · mean 10.77 Gbp per run (median 11.41 Gbp, total 4,880.25 Gbp; 453 runs with a base count) · layout PAIRED 453 · platform ILLUMINA 453 · models Illumina NovaSeq 6000 (453) · 90% of runs with a Sandpiper profile · first public 2025-03-24
Authors (0)
No author record.
Downloads
PRJEB86881.csv.gz (14.3 KB) · parquet (87.7 KB) — all 450 samples, every field with route and confidence · PRJEB86881_determinations.csv.gz (14.9 KB) — 1,800 evidence rows