Infant gut microbiome and norovirus infection, Nicaragua
22 stool samples from infants in León, Nicaragua, longitudinal cohort design; 6 samples associated with gastrointestinal infection/diarrhoea, studying gut microbiome changes before, during, and after norovirus acute gastroenteritis. machine-written summary
22 samples · 24 runs · NI · Infant / toddler · 2022 · 9.17 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 122 sample values (age, collection date, country, feeding mode, health condition, health condition detail, timepoint) |
| ✓ Abstract / description | 22 sample values (location locality) |
| ○ Full text | read; no usable statement or table · PMC9323674 |
| ✓ Supplementary tables | 73 sample values (antibiotic exposure, delivery mode, sex, subject id) |
| – 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
design observational_with_procedure
longitudinal — not resolved
Schedule stated by the source: “Stool collected before, during, and after norovirus acute gastroenteritis per infant (subject letters A-E)”.
Genera, mean relative abundance over 20 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 | 22 | 100% | ||||
| country | 22 | 100% | 22 | |||
| health_condition | 6 | 27% | 6 | |||
| subject_id | 22 | 100% | 22 | |||
| age_at_collection_days | 22 | 100% | 22 | |||
| collection_date | 22 | 100% | 22 | |||
| delivery_mode | 22 | 100% | 22 | |||
| detailed_location | 22 | 100% | ||||
| feeding_mode | 22 | 100% | 22 | |||
| location_locality | 22 | 100% | 22 | |||
| sex | 22 | 100% | 22 | |||
| timepoint_label | 22 | 100% | 22 | |||
| antibiotic_exposure | 7 | 32% | 7 | |||
| health_condition_detail | 6 | 27% | 6 |
- Gut Microbiome Changes Occurring with Norovirus Infection and Recovery in Infants Enrolled in a Longitudinal Birth Cohort in Leon, Nicaragua. PMID 35891376 PMC9323674 curated
- BilR is a gut microbial enzyme that reduces bilirubin to urobilinogen. PMID 38172624 PMC10769871 curated
Archive description
Noroviruses are associated with one fifth of diarrheal illnesses globally and are not yet vaccine preventable. Little is known about the impact norovirus infection has on infant gut microbiome health, which has a role in protecting hosts from pathogens and a probable role in vaccine efficacy. In this study, we characterized infant gut microbiome changes occurring with norovirus AGE and the extent and duration of gut microbiome recovery. Metagenomic sequencing was performed on the stools of 5 infants participating in a longitudinal birth cohort study conducted in Leon, Nicaragua, examining the etiology of viral AGE in children < 2 years old. Taxonomic and functional gut microbiome communities were profiled at time points before, during, and after norovirus AGE for infants experiencing norovirus as their first viral etiology of AGE. Data indicate the trajectory of infant microbiome development was not altered due to norovirus infection. The study provides new insights for developing probiotic treatments and furthering our understanding of the role diarrheal illnesses have in shaping the infant gut microbiome, long-term outcomes, and implications for vaccine efficacy.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler and child by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.title · “Infant gut microbiome changes and”
- body site study.description · “has on infant gut microbiome health, which”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “Infant gut microbiome changes”
- life stage study.description · “viral AGE in children < 2 years”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN29363406 | age_at_collection_days | 341 | R1 | 0.90 | biosample_attr | 341 |
| SAMN29363409 | antibiotic_exposure | yes | R2 | 0.85 | paper.supp.table | Anibioticsreceived=yes |
| SAMN29363406 | collection_date | 2018-08 | R1 | 0.85 | biosample.attribute:collection_date | 2018-08 |
| SAMN29363406 | country | NI | R1 | 0.90 | biosample_attr | Nicaragua: Leon |
| SAMN29363406 | delivery_mode | vaginal | R2 | 0.85 | paper.supp.table | Birth route=Vaginal |
| SAMN29363406 | feeding_mode | mixed | R1 | 0.85 | biosample_attr | breast milk; supplementary nutrition |
| SAMN29363407 | health_condition | gi_infection_or_diarrhoea | R1 | 0.80 | biosample.attribute:gastrointestinal_tract_disorder | gastrointestinal_tract_disorder: acute gastroenteritis |
| SAMN29363407 | health_condition_detail | acute gastroenteritis | R1 | 0.90 | biosample.attribute:gastrointestinal_tract_disorder | gastrointestinal_tract_disorder: acute gastroenteritis |
| SAMN29363406 | location_locality | León | R4 | 0.45 | ena.study_description | birth cohort study conducted in Leon, Nicaragua |
| SAMN29363406 | sex | male | R2 | 0.85 | paper.supp.table | Gender=Male |
| SAMN29363406 | subject_id | PRJNA853174_S1 | R2 | 0.75 | paper.supp.table | Host ID=PRJNA853174_S1 |
| SAMN29363406 | timepoint_label | before | R1 | 0.70 | sample.name_rule:title | A-before |
Sequencing
24 runs over 22 samples · mean 8.81 Gbp per run (median 9.17 Gbp, total 211.54 Gbp; 24 runs with a base count) · layout PAIRED 24 · platform ILLUMINA 24 · models Illumina NovaSeq 6000 (24) · 88% of runs with a Sandpiper profile · first public 2022-06-30
Authors (25)
Cannon JL first · Seabolt MH · Xu R · Montmayeur A · Suh SH · Diez-Valcarce M · Bucardo F · Becker-Dreps S · Vinjé J last · Hall B first · Levy S · Dufault-Thompson K · Arp G · Zhong A · Ndjite GM · Weiss A · Braccia D · Jenkins C · Grant MR · Abeysinghe S · Yang Y · Jermain MD · Wu CH · Ma B · Jiang X last
Downloads
PRJNA853174.csv.gz (1.8 KB) · parquet (71.6 KB) — all 22 samples, every field with route and confidence · PRJNA853174_determinations.csv.gz (3.1 KB) — 217 evidence rows