Diet, Lifestyle and Oral/Gut Microbiota in US Cohort
Cross-sectional study of 32 samples from the USA examining oral (saliva) and gut (stool) microbiota in relation to Western dietary patterns and inflammatory bowel disease status. machine-written summary
32 samples · 32 runs · US · Age unknown · 2013 · 3.03 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 64 sample values (country, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC4050606, PMC5159968, PMC7060530, PMC7702799, PMC8062136, PMC8201803 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 32 sample values (antibiotic exposure) · from BugSigDB |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal — not resolved
8 of 8 people sampled more than once (24 samples; median 3, up to 3 per person).
Genera, mean relative abundance over 24 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 | 32 | 100% | 32 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 32 | 100% | 32 | |||
| antibiotic_exposure | 32 | 100% | 32 |
- A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases. 2021 PMID 34083435 PMC8201803 own_data
- Relating the metatranscriptome and metagenome of the human gut. 2014 PMID 24843156 PMC4050606 own_data
- IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses. 2016 PMID 27986083 PMC5159968 own_data
- Metatranscriptomic analysis to define the Secrebiome, and 16S rRNA profiling of the gut microbiome in obesity and metabolic syndrome of Mexican children. 2020 PMID 32143621 PMC7060530 unsure
- Metagenomics of the modern and historical human oral microbiome with phylogenetic studies on <i>Streptococcus mutans</i> and <i>Streptococcus sobrinus</i>. 2020 PMID 33012228 PMC7702799 unsure
1 more
- Microbial genetic and transcriptional contributions to oxalate degradation by the gut microbiota in health and disease. 2021 PMID 33769280 PMC8062136
Archive description
Associating the biomolecular and metabolic activities of human-associated microbial communities with environment, diet, and conditions such as inflammatory bowel disease remains a significant challenge despite an ever-improving understanding of the human microbiome. This project aims to pilot detection of taxonomic and functional shifts with respect to diet and gastrointestinal disease status in a large prospective cohort: 1. We will establish a reliable and scalable collection method for the oral and gut microbiota. This will determine whether shippable collection kits are comparable to fresh frozen stool and/or saliva samples. 2. We will test the hypothesis that a Western dietary pattern correlates with microbiome community structures or functions enriched in inflammatory bowel disease in either the oral (saliva) or gut (stool) microbiota. By providing methodology to understand the human microbiome from the molecular to the population level, we hope to enable its future use as a diagnostic indicator and as a point of intervention to improve outcomes in IBD and other chronic diseases.
How this project entered the registry
Classified as human gut / stool / oral cavity shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.60. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “human gut metagenome”
- body site run.scientific_name · “human oral metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN01915205 | antibiotic_exposure | no | R2 | 0.60 | external.bugsigdb source | Antibiotics exclusion: 3 months |
| SAMN01915205 | country | US | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea_region | USA |
| SAMN01915205 | subject_id | 310763260 | R1 | 0.70 | sample.name_rule:alias | X310763260_ETOH |
Sequencing
32 runs over 32 samples · mean 2.26 Gbp per run (median 3.03 Gbp, total 72.25 Gbp; 32 runs with a base count) · layout PAIRED 32 · platform ILLUMINA 32 · models Illumina HiSeq 2000 (32) · 94% of runs with a Sandpiper profile · first public 2013-03-12
Authors (74)
Franzosa EA first · Morgan XC · Segata N · Waldron L · Reyes J · Earl AM · Giannoukos G · Boylan MR · Ciulla D · Gevers D · Izard J · Garrett WS · Chan AT · Huttenhower C last · Narayanasamy S first · Jarosz Y · Muller EE · Heintz-Buschart A · Herold M · Kaysen A · Laczny CC · Pinel N · May P · Wilmes P last · Gallardo-Becerra L first · Cornejo-Granados F · García-López R · Valdez-Lara A · Bikel S · Canizales-Quinteros S · López-Contreras BE · Mendoza-Vargas A · Nielsen H · Ochoa-Leyva A last · Liu M first · Devlin JC · Hu J · Volkova A · Battaglia TW · Ho M · Asplin JR · Byrd A · Loke P · Li H · Ruggles KV · Tsirigos A · Blaser MJ · Nazzal L last · Tisza MJ first · Buck CB last · Tarracchini C first · Fontana F · Mancabelli L · Lugli GA · Alessandri G · Turroni F · Ventura M · Milani C 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
PRJNA188481.csv.gz (1.6 KB) · parquet (69.6 KB) — all 32 samples, every field with route and confidence · PRJNA188481_determinations.csv.gz (1.4 KB) — 96 evidence rows