Oropharyngeal microbiome in schizophrenia
32 samples from adults in Maryland, USA, comparing the oropharyngeal microbiome of 16 schizophrenia patients and 16 healthy controls in a case-control study design. machine-written summary
32 samples · 33 runs · US · Adult · 2014 · 5.33 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 159 sample values (age, country, health condition, health condition detail, location region, sex) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 32 sample values (location site) · PMC4556144, PMC5057277 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 64 sample values (antibiotic exposure, health condition, health condition detail) · from HumanMetagenomeDB, Meta2DB (LLNL) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
age: two sequence archives disagree for 1 sample (e.g. 41.6 vs 15190.7) — withheld.
The sources disagree on 1 sample. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).
Contradicted values (1)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN02919214 | age | 41.6 (sequence archive) | 15190.7 (sequence archive) | withheld: neither value published |
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 32 | 100% | ||||
| country | 32 | 100% | 32 | |||
| health_condition | 32 | 100% | 16 | 16 | ||
| subject_id | 0 | 0% | ||||
| antibiotic_exposure | 32 | 100% | 32 | |||
| detailed_location | 32 | 100% | ||||
| health_condition_detail | 32 | 100% | 16 | 16 | ||
| location_region | 32 | 100% | 32 | |||
| location_site | 32 | 100% | 32 | |||
| sex | 32 | 100% | 32 | |||
| age_at_collection_days | 31 | 97% | 31 |
- Composition, taxonomy and functional diversity of the oropharynx microbiome in individuals with schizophrenia and controls. 2015 PMID 26336637 PMC4556144 own_data
- FMAP: Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies. 2016 PMID 27724866 PMC5057277 unsure
Archive description
The microbiome has been shown to alter brain development and modulate behavior and cognition in animals through gut-brain connections, and research in humans suggests that it may be a modulating factor in many disorders. The microbiome has not been extensively studied in individuals with schizophrenia, and little is known about the role the microbiome may play in the pathogenesis of this condition. These samples are part of the first batch of samples that will be analyzed to shed light into the microbial of schizophrenia patients.
How this project entered the registry
Classified as human gut / stool / lower respiratory shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.60. Assay shotgun_dna.
- host run.scientific_name · “human metagenome”
- body site study.description · “microbial of schizophrenia patients”
- body site sample.attr.host_tissue_sampled · “throat swab (n=32/32)”
- life stage sample.attr.host_age · “27.62 (n=30/32)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN02919189 | age_at_collection_days | 21776.2 | R1 | 0.70 | sample.attr.host_age | 59.62 |
| SAMN02919189 | antibiotic_exposure | no | R2 | 0.70 | external.meta2db source | antibiotics: FALSE |
| SAMN02919189 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Maryland |
| SAMN02919205 | health_condition | neurological_psychiatric | R1 | 0.90 | biosample_attr | Schizophrenia |
| SAMN02919189 | health_condition | healthy_control | R2 | 0.70 | external.hmgdb source | HMgDB Diagnosis=control; HMgDB Control=schizophrenia control |
| SAMN02919205 | health_condition_detail | Schizophrenia | R1 | 0.90 | sample.attr.host_disease | Schizophrenia |
| SAMN02919189 | health_condition_detail | control / schizophrenia control | R2 | 0.70 | external.hmgdb source | HMgDB Diagnosis=control; HMgDB Control=schizophrenia control |
| SAMN02919189 | location_region | Maryland | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Maryland |
| SAMN02919189 | location_site | Stanley Research Program at Sheppard Pratt Hospital | R3 | 0.70 | paper.fulltext.methods | Stanley Research Program at Sheppard Pratt Hospital |
| SAMN02919189 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
Sequencing
33 runs over 32 samples · mean 5.97 Gbp per run (median 5.19 Gbp, total 197.08 Gbp; 33 runs with a base count) · layout SINGLE 33 · platform ILLUMINA 33 · models Illumina HiSeq 2000 (33) · 91% of runs with a Sandpiper profile · first public 2014-11-13
Authors (14)
Castro-Nallar E first · Bendall ML · Pérez-Losada M · Sabuncyan S · Severance EG · Dickerson FB · Schroeder JR · Yolken RH · Crandall KA last · Kim J first · Kim MS · Koh AY · Xie Y · Zhan X last
Downloads
PRJNA255439.csv.gz (2.0 KB) · parquet (71.7 KB) — all 32 samples, every field with route and confidence · PRJNA255439_determinations.csv.gz (3.2 KB) — 255 evidence rows