Gut bacteria and tryptophan metabolites in healthy adults, Texas
21 fecal samples from healthy adults in Texas, USA, analyzed with 16S and shotgun sequencing plus LC/MS to study bacterial tryptophan metabolites; cross-sectional design. machine-written summary
21 samples · 21 runs · US · Adult · 2024 · 5.15 Gbp / sample
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what each source gave
| ✓ Sequence archive | 210 sample values (age, collection date, country, health condition, health condition detail, latitude, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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 |
Genera, mean relative abundance over 21 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 | 21 | 100% | ||||
| country | 21 | 100% | 21 | |||
| health_condition | 21 | 100% | 21 | |||
| subject_id | 21 | 100% | 21 | |||
| age_at_collection_days | 21 | 100% | 21 | |||
| collection_date | 21 | 100% | 21 | |||
| detailed_location | 21 | 100% | ||||
| health_condition_detail | 21 | 100% | 21 | |||
| latitude | 21 | 100% | 21 | |||
| location_region | 21 | 100% | 21 | |||
| longitude | 21 | 100% | 21 | |||
| sex | 21 | 100% | 21 |
- Tryptophan Metabolites And Their Predicted Microbial Sources In Fecal Samples Of Healthy Individuals 2023 own_data
Archive description
Tryptophan metabolites (TMs) of bacterial origin are increasingly recognized as important signaling molecules among gut microbiota and with the host. However, few reports exist for fecal TM levels in healthy humans, and reported levels vary widely. Further, the specific bacterial species producing TMs and the combinations of fecal TMs in healthy individuals are not well known. Our research combines 16S and whole genome shotgun sequencing of gut bacteria with a sensitive method (LC/MS) for measuring TMs and a reported method to predict which species are likely TM contributors. To our knowledge, this combination of analyses has not been reported elsewhere and will add significantly to the existing literature. Understanding TM levels and their sources in the healthy intestine are fundamental to elucidating how TMs contribute to maintaining homeostasis. Such knowledge of gut microbiota and their metabolic products will inform novel strategies to maintain intestinal health and prevent or treat dysbioses.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.78. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “fecal samples from healthy humans”
- life stage sample.attr.host_age · “24 (n=20/21)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN40277819 | age_at_collection_days | 12783.8 | R1 | 0.85 | sample.attr.host_age | 35 |
| SAMN40277819 | collection_date | 1993-09-14 | R1 | 0.90 | biosample.attribute:collection_date | 1993-09-14 |
| SAMN40277819 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA:Texas |
| SAMN40277819 | health_condition | healthy_control | R1 | 0.90 | biosample_attr | healthy |
| SAMN40277819 | health_condition_detail | healthy | R1 | 0.90 | sample.attr.host_phenotype | healthy |
| SAMN40277819 | latitude | 29.7052 | R1 | 0.90 | biosample.attribute:lat_lon | 29.705232 N 95.39785 W |
| SAMN40277819 | location_region | Texas | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:Texas |
| SAMN40277819 | longitude | -95.3979 | R1 | 0.90 | biosample.attribute:lat_lon | 29.705232 N 95.39785 W |
| SAMN40277819 | sex | male | R1 | 0.90 | sample.attr.host_sex | male |
| SAMN40277819 | subject_id | 001 | R1 | 0.85 | sample.attr.host_subject_id | 001 |
Sequencing
21 runs over 21 samples · mean 4.92 Gbp per run (median 5.15 Gbp, total 103.27 Gbp; 21 runs with a base count) · layout PAIRED 21 · platform ILLUMINA 21 · models Illumina NovaSeq 6000 (21) · 100% of runs with a Sandpiper profile · first public 2024-03-10
Authors (14)
Chappell CL first · Hoffman KL · Lorenzi PL · Tan L · Petrosino JF · Gibbs RA · Muzny DM · Doddapaneni H · Ross MC · Menon VK · Surathu A · Javornik Cregeen SJ · Reyes AG · Okhuysen PC last
Downloads
PRJNA1084251.csv.gz (1.6 KB) · parquet (71.2 KB) — all 21 samples, every field with route and confidence · PRJNA1084251_determinations.csv.gz (2.2 KB) — 210 evidence rows