Amino acid auxotrophies in German gut microbiome, cross-sectional
190 fecal samples from Germany were analyzed in a cross-sectional study of amino acid auxotrophies in the human gut microbiome, using combined metabolomic, metagenomic, and metabolic modeling approaches. machine-written summary
190 samples · 190 runs · DE · Age unknown · 2023 · 6.08 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 760 sample values (country, latitude, location region, longitude) |
| ✓ Abstract / description | 190 sample values (health condition detail) |
| ○ Full text | read; no usable statement or table · PMC10689445, PMC11228888 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 174 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 | 190 | 100% | 190 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| detailed_location | 190 | 100% | ||||
| health_condition_detail | 190 | 100% | 190 | |||
| latitude | 190 | 100% | 190 | |||
| location_region | 190 | 100% | 190 | |||
| longitude | 190 | 100% | 190 |
- Gut microbial genomes with paired isolates from China illustrate probiotic and cardiometabolic effects. 2024 PMID 38740021 PMC11228888 own_data
- Amino acid auxotrophies in human gut bacteria are linked to higher microbiome diversity and long-term stability. 2023 PMID 37891427 PMC10689445 unsure
Archive description
Amino acid auxotrophies are prevalent among bacteria. They can govern ecological dynamics in microbial communities and indicate metabolic cross-feeding interactions among coexisting genotypes. Despite the ecological importance of auxotrophies, their distribution and impact on the diversity and function of the human gut microbiome remain poorly understood. This study performed the first systematic analysis of the distribution of amino acid auxotrophies in the human gut microbiome using a combined metabolomic, metagenomic, and metabolic modeling approach. Results showed that amino acid auxotrophies are ubiquitous in the colon microbiome, with tryptophan auxotrophy being the most common. Auxotrophy frequencies were found to be higher for those amino acids, that are also essential to the human host. Moreover, a higher overall abundance of auxotrophies was associated with greater microbiome diversity and stability, and the distribution of auxotrophs was found to be related to the human host's metabolome, including trimethylamine oxide, small aromatic acids, and secondary bile acids. Thus, our results suggest that amino acid auxotrophies are important factors that contribute to microbiome ecology and host-microbiome metabolic interactions.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.85. Assay shotgun_dna.
- host study.description · “human gut microbiome remain poorly understood”
- body site run.scientific_name · “human feces metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA112775899 | country | DE | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Germany |
| SAMEA112775899 | health_condition_detail | mixed_case_control: Study analyzes auxotrophies across the human gut microbiome without specifying disease status of sub | R4 | 0.40 | study.description | human gut microbiome |
| SAMEA112775899 | latitude | 54.3227 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 54.3227085 10.135555 |
| SAMEA112775899 | location_region | Schleswig-Holstein | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 54.3227085 10.135555 |
| SAMEA112775899 | longitude | 10.1356 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 54.3227085 10.135555 |
Sequencing
190 runs over 190 samples · mean 6.21 Gbp per run (median 6.08 Gbp, total 1,180.03 Gbp; 190 runs with a base count) · layout PAIRED 183, SINGLE 7 · platform ILLUMINA 190 · models Illumina NovaSeq 6000 (190) · 92% of runs with a Sandpiper profile · first public 2023-03-28
Authors (51)
Starke S first · Harris DMM · Zimmermann J · Schuchardt S · Oumari M · Frank D · Bang C · Rosenstiel P · Schreiber S · Frey N · Franke A · Aden K · Waschina S last · Huang P first · Dong Q · Wang Y · Tian Y · Wang S · Zhang C · Yu L · Tian F · Gao X · Guo H · Yi S · Li M · Liu Y · Zhang Q · Lu W · Wang G · Yang B · Cui S · Hua D · Wang X · Jiao Y · Liu L · Deng Q · Ma B · Wu T · Zou H · Shi J · Zhang H · Fan D · Sheng Y · Zhao J · Tang L · Sun W · CGMR Consortium · Chen W · Kong X · Chen L · Zhai Q last
Help complete this project
3 of the 4 core fields are below 50% coverage: age_category, health_condition, subject_id. Share metadata
Downloads
PRJEB60573.csv.gz (5.4 KB) · parquet (77.0 KB) — all 190 samples, every field with route and confidence · PRJEB60573_determinations.csv.gz (5.5 KB) — 950 evidence rows