Appendicitis microbiome in children/adolescents, Austria
60 samples from children and adolescents with acute appendicitis in Austria (appendix, rectum, and peritoneum), comparing complicated vs. uncomplicated cases in a case-control design. machine-written summary
60 samples · 60 runs · AT · Child · 2022 · 52.3 Mbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 600 sample values (age, collection date, country, health condition, health condition detail, latitude, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 120 sample values (location locality, location site) · PMC9879201 |
| ✓ Supplementary tables | 60 sample values (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
design observational_with_procedure
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 60 | 100% | ||||
| country | 60 | 100% | 60 | |||
| health_condition | 60 | 100% | 60 | |||
| subject_id | 60 | 100% | 60 | |||
| age_at_collection_days | 60 | 100% | 60 | |||
| antibiotic_exposure | 60 | 100% | 60 | |||
| collection_date | 60 | 100% | 60 | |||
| detailed_location | 60 | 100% | ||||
| health_condition_detail | 60 | 100% | 60 | |||
| latitude | 60 | 100% | 60 | |||
| location_locality | 60 | 100% | 60 | |||
| location_region | 60 | 100% | 60 | |||
| location_site | 60 | 100% | 60 | |||
| longitude | 60 | 100% | 60 | |||
| sex | 60 | 100% | 60 |
- Acute appendicitis manifests as two microbiome state types with oral pathogens influencing severity. 2023 PMID 36691230 PMC9879201 own_data
Archive description
Mounting evidence suggests that acute appendicitis (AA) is not one but two diseases, with complicated appendectomy that reaches perforation eventually if untreated and uncomplicated appendectomy which does not. Even though AA is the most frequent cause of surgery from abdominal pain, little is known about the origins and etiopathogenesis of this disease, much less regarding the different disease types. Here, we investigated the microbiome of appendix, stool and peritoneum samples from 60 children and adolescents with AA to assess the composition and potential function of bacteria, archaea and fungi. The microbial community of the appendix revealed a severity-specific shift. This shift was reflected by two major community state types that represented complicated and uncomplicated cases. We demonstrated that complicated, but not uncomplicated, appendicitis is associated with a significant local expansion of oral bacterial pathogens in the appendix, driven by necrotizing Fusobacterium spp., Porphyromonas and Parvimonas. On the contrary, uncomplicated appendicitis was characterized by gut-associated microbiomes. Our findings support the notion of two disease types in AA, which can currently not be distinguished using standard clinical characterizations, nor the analysis of the patient’s stool microbiome. An improved diagnostics could, however, improve non-surgical treatment of uncomplicated AA.
How this project entered the registry
Classified as human blood / tissue / internal fluids / gut / stool / other human site shotgun DNA metagenome of child and adolescent by opus_adjudicated with confidence 0.65. Assay shotgun_dna.
- host study.description · “60 children and adolescents with AA”
- body site study.description · “appendix, stool and peritoneum samples”
- life stage study.description · “60 children and adolescents with AA”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA11050844 | age_at_collection_days | 5844.0 | R1 | 0.70 | sample.attr.host_age | 16 |
| SAMEA11050844 | antibiotic_exposure | no | R2 | 0.80 | paper.supp.Supplementary Tables.xlsx[Supplementary Table 1!Antibiotic_treatment] | P1: Antibiotic_treatment=no |
| SAMEA11050844 | collection_date | 2019-04 | R1 | 0.90 | biosample.attribute:collection_date | 2019-04 |
| SAMEA11050844 | country | AT | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Austria |
| SAMEA11050844 | health_condition | other_disease | R1 | 0.50 | biosample_attr | gangrenous |
| SAMEA11050912 | health_condition | other_disease | R1 | 0.85 | biosample.attribute:host_disease_status | host_disease_status: subacute |
| SAMEA11050844 | health_condition_detail | gangrenous | R1 | 0.90 | sample.attr.host_disease_status | gangrenous |
| SAMEA11050844 | latitude | 47.0707 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 47.0707 15.4395 |
| SAMEA11050844 | location_locality | Graz | R3 | 0.70 | paper.fulltext.methods | Medical University of Graz |
| SAMEA11050844 | location_region | Styria | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 47.0707 15.4395 |
| SAMEA11050844 | location_site | Department of Pediatric and Adolescent Surgery, Medical University of Graz | R3 | 0.70 | paper.fulltext.methods | Department of Pediatric and Adolescent Surgery at the Medical University of Graz |
| SAMEA11050844 | longitude | 15.4395 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 47.0707 15.4395 |
| SAMEA11050844 | sex | male | R1 | 0.90 | sample.attr.host_sex | male |
| SAMEA11050844 | subject_id | ID01 | R1 | 0.85 | sample.attr.host_subject_id | ID01 |
Sequencing
60 runs over 60 samples · mean 52.9 Mbp per run (median 52.3 Mbp, total 3.17 Gbp; 60 runs with a base count) · layout PAIRED 60 · platform ILLUMINA 60 · models Illumina NovaSeq 6000 (60) · 0% of runs with a Sandpiper profile · first public 2022-01-05
Authors (8)
Blohs M first · Mahnert A · Brunnader K · Flucher C · Castellani C · Till H · Singer G · Moissl-Eichinger C last
Downloads
PRJEB49215.csv.gz (2.9 KB) · parquet (74.1 KB) — all 60 samples, every field with route and confidence · PRJEB49215_determinations.csv.gz (6.5 KB) — 780 evidence rows