Urban vs rural gut microbiome, Hunan China, cross-sectional
40 fecal samples from healthy adults in Hunan province, China, comparing gut microbiome composition between recently urbanized and rural subjects in a cross-sectional design. machine-written summary
40 samples · 40 runs · CN · Adult · 2017 · 1.00 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 360 sample values (collection date, country, latitude, lifestyle, lifestyle detail, location region, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 40 sample values (antibiotic exposure) · PMC11069498, PMC11102407, PMC5603068, PMC6198860, PMC8549367, PMC8577285 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 80 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 |
Genera, mean relative abundance over 38 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 | 40 | 100% | ||||
| country | 40 | 100% | 40 | |||
| health_condition | 40 | 100% | 40 | |||
| subject_id | 40 | 100% | 40 | |||
| antibiotic_exposure | 40 | 100% | 40 | |||
| collection_date | 40 | 100% | 40 | |||
| detailed_location | 40 | 100% | ||||
| health_condition_detail | 40 | 100% | 40 | |||
| latitude | 40 | 100% | 40 | |||
| lifestyle | 40 | 100% | 40 | |||
| lifestyle_detail | 40 | 100% | 40 | |||
| location_region | 40 | 100% | 40 | |||
| longitude | 40 | 100% | 40 | |||
| timepoint_label | 40 | 100% | 40 |
- Recent urbanization in China is correlated with a Westernized microbiome encoding increased virulence and antibiotic resistance genes. 2017 PMID 28915922 PMC5603068 own_data
- Indexed variation graphs for efficient and accurate resistome profiling. 2018 PMID 29762644 PMC6198860 own_data
- Geographical separation and ethnic origin influence the human gut microbial composition: a meta-analysis from a Malaysian perspective. 2021 PMID 34463609 PMC8549367 own_data
- HashSeq: a Simple, Scalable, and Conservative De Novo Variant Caller for 16S rRNA Gene Data Sets. 2021 PMID 34751586 PMC8577285 own_data
- MicroPredict: predicting species-level taxonomic abundance of whole-shotgun metagenomic data using only 16S amplicon sequencing data. 2024 PMID 38700829 PMC11102407 unsure
1 more
- Diet-omics in the Study of Urban and Rural Crohn disease Evolution (SOURCE) cohort. 2024 PMID 38704361 PMC11069498
Archive description
The microbiome plays a critical role in host health. Using both 16S rRNA sequencing and whole metagenome sequencing, we compared the gut microbiome of rural and urban people from a single Chinese province, and found significant differences between the community composition of recently urbanized and rural subjects. Microbes that were more abundant in the urban Chinese samples were also more prevalent in an American cohort, suggesting that Westernization of diet and lifestyle can rapidly change the microbiome. Furthermore, the genes encoded by the microbiome and the metabolites generated have significantly altered with urbanization, with an increase in genes associated with resistance and virulence.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.62. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host run.scientific_name · “human gut metagenome(40)”
- body site study.description · “compared the gut microbiome of rural and urban people”
- life stage study.description · “rural and urban people from a single Chinese province”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN05946346 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | antibiotic use within the past 3 months |
| SAMN05946346 | collection_date | 2014-09-25 | R1 | 0.90 | biosample.attribute:collection_date | 2014-09-25 |
| SAMN05946346 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China:Hunan province |
| SAMN05946346 | health_condition | healthy_control | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN05946346 | health_condition_detail | Health | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN05946346 | latitude | 27.4000 | R1 | 0.90 | biosample.attribute:lat_lon | 27.4 N 111.8 E |
| SAMN05946346 | lifestyle | rural_non_industrialized | R1 | 0.85 | biosample.attribute:rural_urban_status | rural |
| SAMN05946346 | lifestyle_detail | rural | R1 | 0.85 | biosample.attribute:rural_urban_status | rural |
| SAMN05946346 | location_region | Hunan | R1 | 0.85 | biosample.attribute:geo_loc_name | China:Hunan province |
| SAMN05946346 | longitude | 111.8000 | R1 | 0.90 | biosample.attribute:lat_lon | 27.4 N 111.8 E |
| SAMN05946346 | subject_id | 1 | R1 | 0.85 | sample.attr.subject_id | 1 |
| SAMN05946346 | timepoint_label | first | R1 | 0.85 | sample.attr.timepoint | first |
Sequencing
40 runs over 40 samples · mean 1.00 Gbp per run (median 1.00 Gbp, total 40.00 Gbp; 40 runs with a base count) · layout SINGLE 40 · platform ILLUMINA 40 · models Illumina HiSeq 4000 (40) · 95% of runs with a Sandpiper profile · first public 2017-12-01
Authors (46)
Winglee K first · Howard AG · Sha W · Gharaibeh RZ · Liu J · Jin D · Fodor AA · Gordon-Larsen P last · Dwiyanto J first · Ayub Q · Lee SM · Foo SC · Chong CW · Rahman S last · Fouladi F first · Young JB · Jang CS first · Kim H · Kim D · Han B last · Braun T first · Feng R · Amir A · Levhar N · Shacham H · Mao R · Hadar R · Toren I · Algavi Y · Abu-Saad K · Zhuo S · Efroni G · Malik A · Picard O · Yavzori M · Agranovich B · Liu TC · Stappenbeck TS · Denson L · Kalter-Leibovici O · Gottlieb E · Borenstein E · Elinav E · Chen M · Ben-Horin S · Haberman Y last
Downloads
PRJNA349463.csv.gz (1.5 KB) · parquet (71.4 KB) — all 40 samples, every field with route and confidence · PRJNA349463_determinations.csv.gz (4.0 KB) — 480 evidence rows