Daily gut microbiota shifts in ICU patients, Baltimore USA
58 longitudinal stool samples from adult ICU patients in Baltimore, USA, sequenced by 16S rRNA and shotgun metagenomics on consecutive days to study temporal fluctuations and microbiota disruption linked to infection risk. machine-written summary
58 samples · 58 runs · US · Adult · 2019 · 4.15 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 290 sample values (collection date, country, location locality, subject id, timepoint) |
| ✓ Abstract / description | 116 sample values (health condition, health condition detail) |
| ○ Full text | read; no usable statement or table · PMC8767333 |
| ○ 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
Other administered intervention (see intervention_detail) design observational_with_procedure · population sepsis_or_infection · Routine ICU antibiotics observed; stool sampled daily, no assigned intervention
“stool samples were collected on consecutive days” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal
9 of 9 people sampled more than once (58 samples; median 6, up to 7 per person) · follow-up median 5 d (max 6 d) · median interval between samples 1 d (time from collection dates). Schedule stated by the source: “stool samples collected on consecutive days” (time origin: unknown).
Each row is one person (9 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 55 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 | 58 | 100% | ||||
| country | 58 | 100% | 58 | |||
| health_condition | 58 | 100% | 58 | |||
| subject_id | 58 | 100% | 58 | |||
| collection_date | 58 | 100% | 58 | |||
| detailed_location | 58 | 100% | ||||
| health_condition_detail | 58 | 100% | 58 | |||
| location_locality | 58 | 100% | 58 | |||
| timepoint_label | 58 | 100% | 58 |
- Context-aware genomic surveillance reveals hidden transmission of a carbapenemase-producing Klebsiella pneumoniae. 2021 PMID 34913861 PMC8767333 own_data
Archive description
Extreme dysbiosis in the gastrointestinal microbiota is frequent in intensive care unit (ICU) patients. This dysbiosis is associated with increased risk of pathobiont colonization and healthcare-associated infections. Researchers have been increasingly interested in developing predictive microbiota disruption indices (MDIs) that could be used to identify patients at risk of poor health outcomes such as gastrointestinal colonization by drug-resistant bacteria or hospital-acquired infections. We used 16S rRNA gene sequencing and shotgun metagenomic sequencing of DNA extracted stool samples. The stool samples were collected on consecutive days. These samples and clinical/epidemiologic data were used to examine temporal patterns in the microbiome. We learned that the microbiota of ICU patients can fluctuate on a daily basis. Gastrointestinal domination by specific bacteria, which is considered a risk factor for infection, was common, variable, and due to both pathogens (e.g., Enterococcus) and commensal bacteria species (e.g., Lactobacillus). Fluctuations in the microbiota were generally what one would predict based on the specific taxa and resistance genes present and antibiotic(s) administered. The rapid changes in the GI microbiota have implications for the design of MDIs for patient monitoring.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “variation in the gastrointestinal microbiota of ICU”
- body site study.description · “dysbiosis in the gastrointestinal microbiota is frequent”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN12617376 | collection_date | 2010-07-13 | R1 | 0.90 | biosample.attribute:collection_date | 2010-07-13 |
| SAMN12617376 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Baltimore |
| SAMN12617376 | health_condition | other_disease | R4 | 0.50 | study.description | intensive care unit (ICU) patients |
| SAMN12617376 | health_condition_detail | ICU patients (critical illness) | R4 | 0.50 | study.description | intensive care unit (ICU) patients |
| SAMN12617376 | location_locality | Baltimore | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Baltimore |
| SAMN12617376 | subject_id | 1113741 | R1 | 0.70 | sample.name_rule:library_name | 1113741_D1_S |
| SAMN12617376 | timepoint_label | D1 | R1 | 0.70 | sample.name_rule:library_name | 1113741_D1_S |
Sequencing
58 runs over 58 samples · mean 4.52 Gbp per run (median 4.15 Gbp, total 262.03 Gbp; 58 runs with a base count) · layout PAIRED 58 · platform ILLUMINA 58 · models Illumina NovaSeq 6000 (58) · 95% of runs with a Sandpiper profile · first public 2019-08-28
Authors (13)
Viehweger A first · Blumenscheit C · Lippmann N · Wyres KL · Brandt C · Hans JB · Hölzer M · Irber L · Gatermann S · Lübbert C · Pletz MW · Holt KE · König B last
Downloads
PRJNA561398.csv.gz (2.6 KB) · parquet (71.9 KB) — all 58 samples, every field with route and confidence · PRJNA561398_determinations.csv.gz (3.6 KB) — 406 evidence rows