Intestinal microbiota in STEC-infected children
Shotgun metagenomic analysis of 14 faecal samples from STEC-infected patients and healthy controls across Italy and Netherlands. Case-control study examining microbiota composition changes during Shiga toxin-producing E. coli O26:H11 infection. machine-written summary
14 samples · 14 runs · IT, NL · Infant / toddler · 2017 · 3.41 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 28 sample values (collection date, country) |
| ○ Abstract / description | read; no usable statement |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| ✓ External resources | 28 sample values (health condition, health condition detail) · from GMrepo v3 |
| – 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
Genera, mean relative abundance over 11 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 | 0 | 0% | ||||
| country | 14 | 100% | 14 | |||
| health_condition | 14 | 100% | 14 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 14 | 100% | 14 | |||
| health_condition_detail | 14 | 100% | 14 |
- (no title) curated
Archive description
The human intestinal microbiota is a homeostatic ecosystem with a remarkable impact on human health and the disruption of this equilibrium leads to an increased susceptibility to infection by numerous pathogens. In this study, we used shotgun metagenomic sequencing and two different bioinformatics approaches, to investigate possible changes in the composition of the intestinal microbiota in samples from patients with STEC infection compared to healthy and healed controls, collected during an outbreak caused by a STEC O26:H11 infection. Regardless of the bioinformatic procedure used, a good resolution of the taxonomic profiles of the samples was achieved. The faeces collected from the STEC infected patients showed a lower intestinal abundance of the beneficial microorganisms Bifidobacterium and Clostridiales spp. in comparison to controls where those microorganisms predominated. These differences were observed with both bioinformatic approaches used and seemed to be related with the STEC infection although the variation in the relative abundance of the members of the Bifidobacterium genus could have also been associated with the dysbiotic status following the diarrhoea.Finally, the metagenomic sequencing allowed to identify in the STEC positive samples, all the virulence traits present in the genomes of the STEC O26 that caused the outbreak. The results shown represent a first evidence of the changes occurring in the intestinal microbiota of children in the course of STEC infection and indicate that metagenomics may be a promising tool for the culture-independent clinical diagnosis of the infection.
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 · “of the human intestinal microbiota in faecal”
- body site study.description · “The human intestinal microbiota is a”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.description · “intestinal microbiota of children in the course”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA104359574 | collection_date | 2015-06-01 | R1 | 0.85 | biosample.attribute:collection_date | 2015-06-01 |
| SAMEA104359574 | country | IT | R1 | 0.90 | biosample_attr | Italy |
| SAMEA104359574 | health_condition | healthy_control | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMEA104359574 | health_condition_detail | Health | R2 | 0.75 | external.gmrepo source | phenotype: Health |
Sequencing
14 runs over 14 samples · mean 3.24 Gbp per run (median 3.41 Gbp, total 45.42 Gbp; 14 runs with a base count) · layout PAIRED 11, SINGLE 3 · platform ILLUMINA 11, ION_TORRENT 3 · models Illumina MiSeq (11), Ion Torrent PGM (3) · 79% of runs with a Sandpiper profile · first public 2017-11-06 – 2018-01-26
Authors (12)
Gigliucci F first · von Meijenfeldt FAB · Knijn A · Michelacci V · Scavia G · Minelli F · Dutilh BE · Ahmad HM · Raangs GC · Friedrich AW · Rossen JWA · Morabito S last
Downloads
PRJEB23207.csv.gz (1.3 KB) · parquet (69.7 KB) — all 14 samples, every field with route and confidence · PRJEB23207_determinations.csv.gz (1.1 KB) — 56 evidence rows