Gut microbiota in MSM vs non-Westernized populations, Essen
Cross-sectional shotgun metagenomics study of 124 gut samples from men who have sex with men in Essen, Germany, linking sexual practices to Prevotellaceae-dominated, non-Westernized-like microbiota composition. machine-written summary
124 samples · 124 runs · DE · Adult · 2024 · 7.43 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,332 sample values (antibiotic exposure, collection date, country, health condition, health condition detail, latitude, location locality, location region) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 124 sample values (location site) · PMC10982974 |
| ✓ Supplementary tables | 191 sample values (diet, medication) |
| – 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 |
sex differs between samples of the same subject id (3 subjects, 6 samples) — sex withheld; subject ids shared by samples of both sexes (3 ids, 6 samples) — ids withheld.
The sources disagree on 6 samples. 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 (12)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN33850128 | sex | female (sequence archive) | subject P015: female in 1 sample, male in 1 sample | withheld: neither value published |
| SAMN33850133 | sex | female (sequence archive) | subject P020: female in 1 sample, male in 1 sample | withheld: neither value published |
| SAMN33850169 | sex | male (sequence archive) | subject P058: male in 1 sample, female in 1 sample | withheld: neither value published |
| SAMN33850185 | sex | male (sequence archive) | subject P015: female in 1 sample, male in 1 sample | withheld: neither value published |
| SAMN33850190 | sex | male (sequence archive) | subject P020: female in 1 sample, male in 1 sample | withheld: neither value published |
| SAMN33850228 | sex | female (sequence archive) | subject P058: male in 1 sample, female in 1 sample | withheld: neither value published |
| SAMN33850128 | subject id | P015 | female (sequence archive) | subject id withheld (samples of both sexes share it) |
| SAMN33850133 | subject id | P020 | female (sequence archive) | subject id withheld (samples of both sexes share it) |
| SAMN33850169 | subject id | P058 | male (sequence archive) | subject id withheld (samples of both sexes share it) |
| SAMN33850185 | subject id | P015 | male (sequence archive) | subject id withheld (samples of both sexes share it) |
| SAMN33850190 | subject id | P020 | male (sequence archive) | subject id withheld (samples of both sexes share it) |
| SAMN33850228 | subject id | P058 | female (sequence archive) | subject id withheld (samples of both sexes share it) |
longitudinal
54 of 64 people sampled more than once (108 samples; median 2, up to 2 per person) · follow-up median 3.5 y (max 3.9 y) · median interval between samples 3.5 y (time from collection dates).
Each row is one person (36 shown of 54); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 113 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 | 124 | 100% | ||||
| country | 124 | 100% | 124 | |||
| health_condition | 105 | 85% | 105 | |||
| subject_id | 118 | 95% | 118 | |||
| collection_date | 124 | 100% | 124 | |||
| detailed_location | 124 | 100% | ||||
| health_condition_detail | 124 | 100% | 124 | |||
| latitude | 124 | 100% | 124 | |||
| location_locality | 124 | 100% | 124 | |||
| location_region | 124 | 100% | 124 | |||
| location_site | 124 | 100% | 124 | |||
| longitude | 124 | 100% | 124 | |||
| medication | 124 | 100% | 124 | |||
| antibiotic_exposure | 123 | 99% | 123 | |||
| sex | 118 | 95% | 118 | |||
| diet | 67 | 54% | 67 |
- Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices. 2024 PMID 38366600 PMC10982974 own_data
Archive description
The human gut microbiota is influenced by various factors, including genetics, health status and environmental conditions, yet, considerable inter-individual differences remain unexplained. Previous studies identified that the gut microbiota of men-having-sex-with-men (MSM) is clearly distinct from that of non-MSM. Here, we reveal through species-level microbiota analysis using shotgun metagenomics that the gut microbiota of many MSM with Western origin resembles gut microbial communities of non-westernized populations. Specifically, MSM gut microbiomes are frequently dominated by members of the Prevotellaceae family including co-colonization of species from the Prevotella copri complex and unknown Prevotellaceae members. Questionnaire-based analysis clarifying inter-individual differences in MSM linked specific sexual practices to microbiota composition. Moreover, machine learning identified microbial features associated with sexual activities in MSM. Together, this study identifies a previously unrecognized role for sexual activities on gut microbiome diversification in MSM, which may have a large impact on population-based microbiota studies.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “of a non-Westernized gut microbiota in men”
- body site study.description · “The human gut microbiota is influenced”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- life stage study.title · “gut microbiota in men who have sex”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN33850114 | antibiotic_exposure | no | R1 | 0.90 | biosample_attr | no |
| SAMN33850117 | antibiotic_exposure | yes | R1 | 0.80 | sample.attr.antibiotics_use_6months | yes |
| SAMN33850114 | collection_date | 2016-03-15 | R1 | 0.90 | biosample.attribute:collection_date | 2016-03-15 |
| SAMN33850114 | country | DE | R1 | 0.90 | sample.attr.geo_loc_name | Germany: Essen |
| SAMN33850171 | diet | omnivore | R2 | 0.85 | paper.supp.mmc2.xlsx[Sheet1!diet] | no |
| SAMN33850114 | health_condition | other_infection | R1 | 0.90 | biosample_attr | positive |
| SAMN33850114 | health_condition_detail | positive | R1 | 0.90 | sample.attr.hiv_status | positive |
| SAMN33850114 | latitude | 51.4361 | R1 | 0.90 | biosample.attribute:lat_lon | 51.4361 N 6.9895 E |
| SAMN33850114 | location_locality | Essen | R1 | 0.85 | biosample.attribute:geo_loc_name | Germany: Essen |
| SAMN33850114 | location_region | North Rhine-Westphalia | R1 | 0.60 | biosample.attribute:lat_lon | 51.4361 N 6.9895 E |
| SAMN33850114 | location_site | Clinic of Dermatology, Department of Venerology, University Hospital Essen | R3 | 0.70 | paper.fulltext.methods | Clinic of Dermatology, Department of Venerology of the University Hospital Essen |
| SAMN33850114 | longitude | 6.9895 | R1 | 0.90 | biosample.attribute:lat_lon | 51.4361 N 6.9895 E |
| SAMN33850114 | medication | antiretroviral | R2 | 0.85 | paper.supp.mmc2.xlsx[Sheet1!Antiretroviral therapy (ART)] | yes |
| SAMN33850114 | sex | male | R1 | 0.90 | sample.attr.sex | male |
| SAMN33850114 | subject_id | P001 | R1 | 0.70 | sample.name_rule:alias | P001L1 |
Sequencing
124 runs over 124 samples · mean 7.64 Gbp per run (median 7.43 Gbp, total 947.04 Gbp; 124 runs with a base count) · layout PAIRED 124 · platform ILLUMINA 124 · models Illumina NovaSeq 6000 (124) · 91% of runs with a Sandpiper profile · first public 2024-02-25
Authors (15)
Huang KD first · Amend L · Gálvez EJC · Lesker TR · de Oliveira R · Bielecka A · Blanco-Míguez A · Valles-Colomer M · Ruf I · Pasolli E · Buer J · Segata N · Esser S · Strowig T · Kehrmann J last
Downloads
PRJNA947377.csv.gz (5.3 KB) · parquet (78.3 KB) — all 124 samples, every field with route and confidence · PRJNA947377_determinations.csv.gz (11.5 KB) — 1,647 evidence rows