Gut microbiota function in healthy Sardinian adults
Cross-sectional study of 15 gut microbiome samples from healthy adults in Italy (Sardinia), using shotgun metagenomics and metaproteomics to compare genetic potential and active functions of the gut microbiota. machine-written summary
15 samples · 38 runs · IT · Adult · 2017 · 1.34 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 75 sample values (collection date, country, latitude, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 15 sample values (subject id) · PMC11240238, PMC5037606, PMC5513205 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 30 sample values (health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 13 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 | 15 | 100% | ||||
| country | 15 | 100% | 15 | |||
| health_condition | 15 | 100% | 15 | |||
| subject_id | 15 | 100% | 15 | |||
| collection_date | 15 | 100% | 15 | |||
| detailed_location | 15 | 100% | ||||
| health_condition_detail | 15 | 100% | 15 | |||
| latitude | 15 | 100% | 15 | |||
| location_region | 15 | 100% | 15 | |||
| longitude | 15 | 100% | 15 |
- The impact of sequence database choice on metaproteomic results in gut microbiota studies. 2016 PMID 27671352 PMC5037606 own_data
- Potential and active functions in the gut microbiota of a healthy human cohort. 2017 PMID 28709472 PMC5513205 own_data
- gNOMO2: a comprehensive and modular pipeline for integrated multi-omics analyses of microbiomes. 2024 PMID 38995144 PMC11240238 own_data
Archive description
Gut microbiome research is rapidly moving towards the functional characterization of the microbiota by means of shotgun meta-omics. Here, we selected a cohort of healthy subjects from an indigenous and monitored Sardinian population to analyze their gut microbiota using both shotgun metagenomics and shotgun metaproteomics. We found a considerable divergence between genetic potential and functional activity of the human healthy gut microbiota, in spite of a quite comparable taxonomic structure revealed by the two approaches. Investigation of inter-individual variability of taxonomic features revealed Bacteroides and Akkermansia as remarkably conserved and variable in abundance within the population, respectively. Firmicutes-driven butyrogenesis (mainly due to Faecalibacterium spp.) was shown to be the functional activity with the higher expression rate and the lower inter-individual variability in the study cohort, highlighting the key importance of the biosynthesis of this microbial by-product for the gut homeostasis. The taxon-specific contribution to functional activities and metabolic tasks was also examined, giving insights into the peculiar role of several gut microbiota members in carbohydrate metabolism (including polysaccharide degradation, glycan transport, glycolysis and short-chain fatty acid production). In conclusion, our results provide useful indications regarding the main functions actively exerted by the gut microbiota members of a healthy human cohort, and support metaproteomics as a valuable approach to investigate the functional role of the gut microbiota in health and disease.
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 · “functions in the gut microbiota of a”
- body site study.description · “Gut microbiome research is”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA53400418 | collection_date | 2014 | R1 | 0.90 | biosample.attribute:collection_date | 2014 |
| SAMEA53400418 | country | IT | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Italy |
| SAMEA53400418 | health_condition | healthy_control | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMEA53400418 | health_condition_detail | Health | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMEA53400418 | latitude | 39.8833 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 39°53′N 9°33′E |
| SAMEA53400418 | location_region | Sardinia | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 39°53′N 9°33′E |
| SAMEA53400418 | longitude | 9.5500 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 39°53′N 9°33′E |
| SAMEA53400418 | subject_id | SAMEA53400418 | R3 | 0.75 | design.one_sample_per_subject:fulltext | a stool sample was collected from each subject, and its metagenome and metaproteome were characterized |
Sequencing
38 runs over 15 samples · mean 0.64 Gbp per run (median 0.74 Gbp, total 24.47 Gbp; 38 runs with a base count) · layout PAIRED 38 · platform ILLUMINA 38 · models Illumina HiScanSQ (38) · 87% of runs with a Sandpiper profile · first public 2017-07-05
Authors (26)
Tanca A first · Palomba A · Fraumene C · Pagnozzi D · Manghina V · Deligios M · Muth T · Rapp E · Martens L · Addis MF · Uzzau S last · Abbondio M · Cucca F · Fiorillo E · Ormaasen I first · Rudi K · Diep DB · Snipen L last · Arikan M first · Tarracchini C first · Lugli GA · Mancabelli L · van Sinderen D · Turroni F · Ventura M · Milani C last
Downloads
PRJEB19090.csv.gz (1.3 KB) · parquet (70.5 KB) — all 15 samples, every field with route and confidence · PRJEB19090_determinations.csv.gz (1.7 KB) — 120 evidence rows