Gut archaeome survey of Methanomassiliicoccales, UK samples
Cross-sectional study of 130 samples from the United Kingdom examining Methanomassiliicoccales archaea in the human gut and their association with trimethylamine-producing bacteria. machine-written summary
130 samples · 130 runs · GB · Age unknown · 2022 · 0.68 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 650 sample values (collection date, country, latitude, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC7883539 |
| ○ 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 114 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 | 130 | 100% | 130 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| collection_date | 130 | 100% | 130 | |||
| detailed_location | 130 | 100% | ||||
| latitude | 130 | 100% | 130 | |||
| location_region | 130 | 100% | 130 | |||
| longitude | 130 | 100% | 130 |
- Genomic Insights into Adaptations of Trimethylamine-Utilizing Methanogens to Diverse Habitats, Including the Human Gut. 2021 PMID 33563787 PMC7883539 own_data
- Codiversification of gut microbiota with humans. 2022 PMID 36108023 PMC10777373 unsure
Archive description
Methanomassiliicoccales are a lesser known component of the human gut microbiota. This archaeal order is composed of methane producers that use methylated amines, such as trimethylamine, in methane production. This group has only one cultured representative how they adapted to inhabit the mammalian gut and how they interact with other microbes is largely unknown. Using bioinformatics methods applied to DNA from a wide range of samples, we profiled the relative abundances of these archaea in environmental and host-associated microbial communities. We observed two groups of Methanomassiliicoccales, one largely host-associated and one largely found in environmental samples, with some exceptions. When host-associated, these archaea have a distinct set of genes related to adhesion and possess genes related to bile resistance. We did not detect Methanomassiliicoccales in all human populations tested but when present, they are correlated with Bacteria known to produce trimethylamine. Since trimethylamine is linked to cardiovascular disease risk, these intriguing Archaea may also be involved.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.60. Assay shotgun_dna.
- host study.description · “lesser known component of the human gut microbiota”
- body site study.title · “adaptations of TMA-utilizing methanogens”
- body site study.description · “inhabit the mammalian gut”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA7294443 | collection_date | 2017-12-12 | R1 | 0.90 | biosample.attribute:collection_date | 2017-12-12 |
| SAMEA7294443 | country | GB | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | United Kingdom |
| SAMEA7294443 | latitude | 51.4974 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 51.497437 -0.119738 |
| SAMEA7294443 | location_region | England | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 51.497437 -0.119738 |
| SAMEA7294443 | longitude | -0.1197 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 51.497437 -0.119738 |
Sequencing
130 runs over 130 samples · mean 0.76 Gbp per run (median 0.68 Gbp, total 98.79 Gbp; 130 runs with a base count) · layout PAIRED 130 · platform ILLUMINA 130 · models Illumina HiSeq 3000 (130) · 88% of runs with a Sandpiper profile · first public 2022-01-05 – 2022-07-12
Authors (26)
de la Cuesta-Zuluaga J first · Spector TD · Youngblut ND · Ley RE last · Suzuki TA first · Fitzstevens JL · Schmidt VT · Enav H · Huus KE · Mbong Ngwese M · Grießhammer A · Pfleiderer A · Adegbite BR · Zinsou JF · Esen M · Velavan TP · Adegnika AA · Song LH · Muehlbauer AL · Marchi N · Kang H · Maier L · Blekhman R · Ségurel L · Ko G · Kremsner P
Help complete this project
3 of the 4 core fields are below 50% coverage: age_category, health_condition, subject_id. Share metadata
Downloads
PRJEB40256.csv.gz (4.2 KB) · parquet (75.0 KB) — all 130 samples, every field with route and confidence · PRJEB40256_determinations.csv.gz (4.8 KB) — 650 evidence rows