Gut microbiome LPS and TLR4 signaling in healthy US adults
Cross-sectional study of 10 fecal samples from healthy adults in Cambridge, USA, examining TLR4 signaling activity of gut microbiota-derived lipopolysaccharide, compared with Human Microbiome Project metagenomic data. machine-written summary
10 samples · 10 runs · US · Adult · 2017 · 5.39 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 80 sample values (collection date, country, health condition, health condition detail, latitude, location locality, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC5686520 |
| ○ 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 |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 9 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 | 10 | 100% | ||||
| country | 10 | 100% | 10 | |||
| health_condition | 10 | 100% | 10 | |||
| subject_id | 10 | 100% | 10 | |||
| collection_date | 10 | 100% | 10 | |||
| detailed_location | 10 | 100% | ||||
| health_condition_detail | 10 | 100% | 10 | |||
| latitude | 10 | 100% | 10 | |||
| location_locality | 10 | 100% | 10 | |||
| longitude | 10 | 100% | 10 |
- Total Lipopolysaccharide from the Human Gut Microbiome Silences Toll-Like Receptor Signaling. 2017 PMID 29152585 PMC5686520 own_data
Archive description
We performed computational and experimental analysis of healthy human fecal samples to examine the TLR4 signaling capacity of the gut microbiota. This analysis revealed that an immuno-inhibitory activity of LPS, conserved across the Bacteroidales and derived from an under-acylated structural feature, silences TLR4 signaling for the entire consortium of organisms inhabiting the human gut. Comparative analysis of metagenomic data from the Human Microbiome Project and healthy donor samples indicates that immune silencing via LPS is a microbe intrinsic feature in all healthy adults.
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.scientific_name · “human gut metagenome”
- body site study.description · “healthy human fecal samples”
- life stage study.description · “microbe intrinsic feature in all healthy adults”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN07792073 | collection_date | 2015-11 | R1 | 0.90 | biosample.attribute:collection_date | 2015-11 |
| SAMN07792073 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Cambridge |
| SAMN07792073 | health_condition | healthy_control | R1 | 0.85 | biosample.attribute:isolation_source | feces |
| SAMN07792073 | health_condition_detail | feces | R1 | 0.85 | biosample.attribute:isolation_source | feces |
| SAMN07792073 | latitude | 42.3700 | R1 | 0.90 | biosample.attribute:lat_lon | 42.37 N 71.10 W |
| SAMN07792073 | location_locality | Cambridge | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Cambridge |
| SAMN07792073 | longitude | -71.1000 | R1 | 0.90 | biosample.attribute:lat_lon | 42.37 N 71.10 W |
| SAMN07792073 | subject_id | donor 1 | R1 | 0.85 | biosample.attribute:host | human donor 1 |
Sequencing
10 runs over 10 samples · mean 6.00 Gbp per run (median 5.39 Gbp, total 60.04 Gbp; 10 runs with a base count) · layout PAIRED 10 · platform ILLUMINA 10 · models Illumina HiSeq 2500 (10) · 90% of runs with a Sandpiper profile · first public 2017-10-18
Authors (21)
d'Hennezel E first · Abubucker S · Murphy LO · Cullen TW last · Argentini C first · Lugli GA · Tarracchini C · Fontana F · Mancabelli L · Viappiani A · Anzalone R · Angelini L · Alessandri G · Longhi G · Bianchi MG · Taurino G · Bussolati O · Milani C · van Sinderen D · Turroni F · Ventura M last
Downloads
PRJNA414479.csv.gz (1.2 KB) · parquet (70.2 KB) — all 10 samples, every field with route and confidence · PRJNA414479_determinations.csv.gz (1.1 KB) — 80 evidence rows