HTTP 200 OK
Allow: GET, HEAD, OPTIONS
Content-Type: application/json
Vary: Accept
{
"links": {
"first": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Host-associated:Human:Digestive%20system:Oral:Subgingival%20plaque/studies?format=api&page=1",
"last": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Host-associated:Human:Digestive%20system:Oral:Subgingival%20plaque/studies?format=api&page=1",
"next": null,
"prev": null
},
"data": [
{
"type": "studies",
"id": "MGYS00006366",
"attributes": {
"accession": "MGYS00006366",
"bioproject": "PRJEB56435",
"samples-count": 24,
"is-private": false,
"last-update": "2024-03-15T15:48:23",
"secondary-accession": "ERP141374",
"centre-name": "EMG",
"public-release-date": null,
"study-abstract": "The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA548383, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Subgingival plaque.",
"study-name": "EMG produced TPA metagenomics assembly of PRJNA548383 data set (Subgingival Microbiome of Tobacco Cigarette Smokers with and without Periodontal Disease).",
"data-origination": "SUBMITTED"
},
"relationships": {
"downloads": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006366/downloads?format=api"
}
},
"geocoordinates": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006366/geocoordinates?format=api"
}
},
"analyses": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006366/analyses?format=api"
}
},
"biomes": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006366/biomes?format=api"
},
"data": [
{
"type": "biomes",
"id": "root:Host-associated:Human:Digestive system:Oral:Subgingival plaque",
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Host-associated:Human:Digestive%20system:Oral:Subgingival%20plaque?format=api"
}
}
]
},
"publications": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006366/publications?format=api"
}
},
"samples": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006366/samples?format=api"
}
}
},
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006366?format=api"
}
},
{
"type": "studies",
"id": "MGYS00006365",
"attributes": {
"accession": "MGYS00006365",
"bioproject": "PRJEB56431",
"samples-count": 68,
"is-private": false,
"last-update": "2023-09-02T10:50:52",
"secondary-accession": "ERP141370",
"centre-name": "EMG",
"public-release-date": null,
"study-abstract": "The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA552294, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Subgingival plaque.",
"study-name": "EMG produced TPA metagenomics assembly of PRJNA552294 data set (Subgingival metagenome of aggressive periodontitis).",
"data-origination": "SUBMITTED"
},
"relationships": {
"downloads": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006365/downloads?format=api"
}
},
"geocoordinates": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006365/geocoordinates?format=api"
}
},
"analyses": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006365/analyses?format=api"
}
},
"biomes": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006365/biomes?format=api"
},
"data": [
{
"type": "biomes",
"id": "root:Host-associated:Human:Digestive system:Oral:Subgingival plaque",
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Host-associated:Human:Digestive%20system:Oral:Subgingival%20plaque?format=api"
}
}
]
},
"publications": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006365/publications?format=api"
}
},
"samples": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006365/samples?format=api"
}
}
},
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006365?format=api"
}
},
{
"type": "studies",
"id": "MGYS00006307",
"attributes": {
"accession": "MGYS00006307",
"bioproject": "PRJEB56428",
"samples-count": 22,
"is-private": false,
"last-update": "2023-09-01T15:17:52",
"secondary-accession": "ERP141367",
"centre-name": "EMG",
"public-release-date": null,
"study-abstract": "The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA597465, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Subgingival plaque.",
"study-name": "EMG produced TPA metagenomics assembly of PRJNA597465 data set (Species Level Characterization of Dental Plaque Associated Microbiome of Native Indian Children using Metagenome Sequencing).",
"data-origination": "SUBMITTED"
},
"relationships": {
"downloads": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006307/downloads?format=api"
}
},
"geocoordinates": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006307/geocoordinates?format=api"
}
},
"analyses": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006307/analyses?format=api"
}
},
"biomes": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006307/biomes?format=api"
},
"data": [
{
"type": "biomes",
"id": "root:Host-associated:Human:Digestive system:Oral:Subgingival plaque",
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Host-associated:Human:Digestive%20system:Oral:Subgingival%20plaque?format=api"
}
}
]
},
"publications": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006307/publications?format=api"
}
},
"samples": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006307/samples?format=api"
}
}
},
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006307?format=api"
}
},
{
"type": "studies",
"id": "MGYS00006315",
"attributes": {
"accession": "MGYS00006315",
"bioproject": "PRJEB56433",
"samples-count": 25,
"is-private": false,
"last-update": "2023-09-01T13:25:52",
"secondary-accession": "ERP141372",
"centre-name": "EMG",
"public-release-date": null,
"study-abstract": "The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA508385, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Subgingival plaque.",
"study-name": "EMG produced TPA metagenomics assembly of PRJNA508385 data set (Comparative metagenomics reveals taxonomically idiosyncratic yet functionally congruent communities in periodontitis).",
"data-origination": "SUBMITTED"
},
"relationships": {
"downloads": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006315/downloads?format=api"
}
},
"geocoordinates": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006315/geocoordinates?format=api"
}
},
"analyses": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006315/analyses?format=api"
}
},
"biomes": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006315/biomes?format=api"
},
"data": [
{
"type": "biomes",
"id": "root:Host-associated:Human:Digestive system:Oral:Subgingival plaque",
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Host-associated:Human:Digestive%20system:Oral:Subgingival%20plaque?format=api"
}
}
]
},
"publications": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006315/publications?format=api"
}
},
"samples": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006315/samples?format=api"
}
}
},
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006315?format=api"
}
},
{
"type": "studies",
"id": "MGYS00005651",
"attributes": {
"accession": "MGYS00005651",
"bioproject": "PRJEB40715",
"samples-count": 4,
"is-private": false,
"last-update": "2020-11-17T18:52:20",
"secondary-accession": "ERP124374",
"centre-name": "EMG",
"public-release-date": null,
"study-abstract": "The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA78025, and was assembled with metaSPAdes v3.14.1, SPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Subgingival plaque.",
"study-name": "EMG produced TPA metagenomics assembly of PRJNA78025 data set (Human Oral Subgingival Plaque Microbiome).",
"data-origination": "SUBMITTED"
},
"relationships": {
"downloads": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00005651/downloads?format=api"
}
},
"geocoordinates": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00005651/geocoordinates?format=api"
}
},
"analyses": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00005651/analyses?format=api"
}
},
"biomes": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00005651/biomes?format=api"
},
"data": [
{
"type": "biomes",
"id": "root:Host-associated:Human:Digestive system:Oral:Subgingival plaque",
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Host-associated:Human:Digestive%20system:Oral:Subgingival%20plaque?format=api"
}
}
]
},
"publications": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00005651/publications?format=api"
}
},
"samples": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00005651/samples?format=api"
}
}
},
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00005651?format=api"
}
},
{
"type": "studies",
"id": "MGYS00005655",
"attributes": {
"accession": "MGYS00005655",
"bioproject": "PRJNA78025",
"samples-count": 4,
"is-private": false,
"last-update": "2020-11-17T18:40:42",
"secondary-accession": "SRP018108",
"centre-name": "Center for Bioinformatics and Computational Biology",
"public-release-date": null,
"study-abstract": "The oral microbiome, the complex ecosystem of microbes inhabiting the human mouth, harbors several thousands of bacterial types. The proliferation of pathogenic bacteria within the mouth gives rise to periodontitis, an inflammatory disease known to also constitute a risk factor for cardiovascular disease. While much is known about individual species associated with pathogenesis, the system-level mechanisms underlying the transition from health to disease are still poorly understood. Our pilot study demonstrates the power of high-throughput sequencing as a tool for understanding the role of the oral microbiome in periodontal disease. After the removal of supragingival plaque with sterile gauze, individual subgingival plaque samples were taken from the meio-buccal aspect of four molar teeth in four quadrants per subject using sterile periodontal curettes. Bacterial DNA extraction was performed using commercially available DNA purification kit. For 16S rRNA sequencing, DNA samples were amplified using specific primers and sequenced by 454 machines. Metagenomic shotgun sequences were obtained from the Illumina instruments.",
"study-name": "Human Oral Subgingival Plaque Microbiome",
"data-origination": "HARVESTED"
},
"relationships": {
"downloads": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00005655/downloads?format=api"
}
},
"geocoordinates": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00005655/geocoordinates?format=api"
}
},
"analyses": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00005655/analyses?format=api"
}
},
"biomes": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00005655/biomes?format=api"
},
"data": [
{
"type": "biomes",
"id": "root:Host-associated:Human:Digestive system:Oral:Subgingival plaque",
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Host-associated:Human:Digestive%20system:Oral:Subgingival%20plaque?format=api"
}
}
]
},
"publications": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00005655/publications?format=api"
}
},
"samples": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00005655/samples?format=api"
}
}
},
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00005655?format=api"
}
},
{
"type": "studies",
"id": "MGYS00003719",
"attributes": {
"accession": "MGYS00003719",
"bioproject": "PRJNA419453",
"samples-count": 21,
"is-private": false,
"last-update": "2019-11-07T16:56:01",
"secondary-accession": "SRP125475",
"centre-name": "Peking University Health Science Center",
"public-release-date": null,
"study-abstract": "The microbial community diversities of subgingival plaque from 3 health subjects, 3 CP patients, 3 AgP patients.",
"study-name": "microbial community diversities of subgingival plaque of 9 subjects",
"data-origination": "HARVESTED"
},
"relationships": {
"downloads": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00003719/downloads?format=api"
}
},
"geocoordinates": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00003719/geocoordinates?format=api"
}
},
"analyses": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00003719/analyses?format=api"
}
},
"biomes": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00003719/biomes?format=api"
},
"data": [
{
"type": "biomes",
"id": "root:Host-associated:Human:Digestive system:Oral:Subgingival plaque",
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Host-associated:Human:Digestive%20system:Oral:Subgingival%20plaque?format=api"
}
}
]
},
"publications": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00003719/publications?format=api"
}
},
"samples": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00003719/samples?format=api"
}
}
},
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00003719?format=api"
}
},
{
"type": "studies",
"id": "MGYS00002395",
"attributes": {
"accession": "MGYS00002395",
"bioproject": "PRJNA416501",
"samples-count": 68,
"is-private": false,
"last-update": "2019-11-07T16:55:59",
"secondary-accession": "SRP123221",
"centre-name": "Universite de Rennes 1",
"public-release-date": null,
"study-abstract": "Chronic periodontitis subgingival samples in patients with HFE C282Y hemochromatosis.",
"study-name": "Hemoparo",
"data-origination": "HARVESTED"
},
"relationships": {
"downloads": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002395/downloads?format=api"
}
},
"geocoordinates": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002395/geocoordinates?format=api"
}
},
"analyses": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002395/analyses?format=api"
}
},
"biomes": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002395/biomes?format=api"
},
"data": [
{
"type": "biomes",
"id": "root:Host-associated:Human:Digestive system:Oral:Subgingival plaque",
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Host-associated:Human:Digestive%20system:Oral:Subgingival%20plaque?format=api"
}
}
]
},
"publications": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002395/publications?format=api"
}
},
"samples": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002395/samples?format=api"
}
}
},
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002395?format=api"
}
},
{
"type": "studies",
"id": "MGYS00002394",
"attributes": {
"accession": "MGYS00002394",
"bioproject": "PRJNA271538",
"samples-count": 20,
"is-private": false,
"last-update": "2019-11-07T16:55:54",
"secondary-accession": "SRP051741",
"centre-name": "Peking University School and Hospital of Stomatology",
"public-release-date": null,
"study-abstract": "First permanent molars frequently present severe conditions in periodontitis cases. Implant restoration is an accepted means of replacing teeth lost due to periodontitis. The present investigation focused on the microbiome analysis of 10 healthy dental implants and 10 chronic periodontitis patients using 454-prosequencing of 16S rDNA. Subgingival plaque and peri-implant biofilm were sampled at the first permanent molar site before and after implant restoration.",
"study-name": "Subgingival plaque and peri-implant biofilm",
"data-origination": "HARVESTED"
},
"relationships": {
"downloads": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002394/downloads?format=api"
}
},
"geocoordinates": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002394/geocoordinates?format=api"
}
},
"analyses": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002394/analyses?format=api"
}
},
"biomes": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002394/biomes?format=api"
},
"data": [
{
"type": "biomes",
"id": "root:Host-associated:Human:Digestive system:Oral:Subgingival plaque",
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Host-associated:Human:Digestive%20system:Oral:Subgingival%20plaque?format=api"
}
}
]
},
"publications": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002394/publications?format=api"
}
},
"samples": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002394/samples?format=api"
}
}
},
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002394?format=api"
}
},
{
"type": "studies",
"id": "MGYS00002274",
"attributes": {
"accession": "MGYS00002274",
"bioproject": "PRJNA335630",
"samples-count": 10,
"is-private": false,
"last-update": "2019-11-07T16:55:52",
"secondary-accession": "SRP080750",
"centre-name": "Medical University of Graz",
"public-release-date": null,
"study-abstract": "In five ten-year-old children, biofilm was collected from the upper first premolars and first molars using sterilized, UV-treated paper points inserted into the subgingival sulcus at eight sites.",
"study-name": "human oral metagenome Metagenome",
"data-origination": "HARVESTED"
},
"relationships": {
"downloads": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002274/downloads?format=api"
}
},
"geocoordinates": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002274/geocoordinates?format=api"
}
},
"analyses": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002274/analyses?format=api"
}
},
"biomes": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002274/biomes?format=api"
},
"data": [
{
"type": "biomes",
"id": "root:Host-associated:Human:Digestive system:Oral:Subgingival plaque",
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Host-associated:Human:Digestive%20system:Oral:Subgingival%20plaque?format=api"
}
}
]
},
"publications": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002274/publications?format=api"
}
},
"samples": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002274/samples?format=api"
}
}
},
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002274?format=api"
}
},
{
"type": "studies",
"id": "MGYS00002272",
"attributes": {
"accession": "MGYS00002272",
"bioproject": "PRJNA292354",
"samples-count": 40,
"is-private": false,
"last-update": "2019-11-07T16:55:50",
"secondary-accession": "SRP073270",
"centre-name": "UCLA School of Dentistry",
"public-release-date": null,
"study-abstract": "",
"study-name": "healthy and stomatitis denture microbiome",
"data-origination": "HARVESTED"
},
"relationships": {
"downloads": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002272/downloads?format=api"
}
},
"geocoordinates": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002272/geocoordinates?format=api"
}
},
"analyses": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002272/analyses?format=api"
}
},
"biomes": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002272/biomes?format=api"
},
"data": [
{
"type": "biomes",
"id": "root:Host-associated:Human:Digestive system:Oral:Subgingival plaque",
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Host-associated:Human:Digestive%20system:Oral:Subgingival%20plaque?format=api"
}
}
]
},
"publications": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002272/publications?format=api"
}
},
"samples": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002272/samples?format=api"
}
}
},
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002272?format=api"
}
},
{
"type": "studies",
"id": "MGYS00002269",
"attributes": {
"accession": "MGYS00002269",
"bioproject": "PRJNA289294",
"samples-count": 147,
"is-private": false,
"last-update": "2019-11-07T16:55:48",
"secondary-accession": "SRP062274",
"centre-name": "Academic Centre for Dentistry Amsterdam",
"public-release-date": null,
"study-abstract": "Subgingival microbiome in relation to clinical outcomes after the use of antibiotics in the treatment of periodontitis.",
"study-name": "Subgingival microbiome Metagenome",
"data-origination": "HARVESTED"
},
"relationships": {
"downloads": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002269/downloads?format=api"
}
},
"geocoordinates": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002269/geocoordinates?format=api"
}
},
"analyses": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002269/analyses?format=api"
}
},
"biomes": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002269/biomes?format=api"
},
"data": [
{
"type": "biomes",
"id": "root:Host-associated:Human:Digestive system:Oral:Subgingival plaque",
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Host-associated:Human:Digestive%20system:Oral:Subgingival%20plaque?format=api"
}
}
]
},
"publications": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002269/publications?format=api"
}
},
"samples": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002269/samples?format=api"
}
}
},
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002269?format=api"
}
},
{
"type": "studies",
"id": "MGYS00002257",
"attributes": {
"accession": "MGYS00002257",
"bioproject": "PRJNA244164",
"samples-count": 1,
"is-private": false,
"last-update": "2019-11-07T16:55:46",
"secondary-accession": "SRP041078",
"centre-name": "University of Otago",
"public-release-date": null,
"study-abstract": "Characterization of the Dental Plaques of axial spondyloarthiritis patients",
"study-name": "Dental Plaque 16s rRNA v6 amplicons",
"data-origination": "HARVESTED"
},
"relationships": {
"downloads": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002257/downloads?format=api"
}
},
"geocoordinates": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002257/geocoordinates?format=api"
}
},
"analyses": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002257/analyses?format=api"
}
},
"biomes": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002257/biomes?format=api"
},
"data": [
{
"type": "biomes",
"id": "root:Host-associated:Human:Digestive system:Oral:Subgingival plaque",
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Host-associated:Human:Digestive%20system:Oral:Subgingival%20plaque?format=api"
}
}
]
},
"publications": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002257/publications?format=api"
}
},
"samples": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002257/samples?format=api"
}
}
},
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002257?format=api"
}
},
{
"type": "studies",
"id": "MGYS00002229",
"attributes": {
"accession": "MGYS00002229",
"bioproject": "PRJNA269205",
"samples-count": 100,
"is-private": false,
"last-update": "2019-11-07T16:55:44",
"secondary-accession": "SRP051201",
"centre-name": "University of Florida",
"public-release-date": null,
"study-abstract": "16S sequencing of subgingival microbiota from subjects with chronic periodontitis and healthy subjects.",
"study-name": "Human oral subgingival communities",
"data-origination": "HARVESTED"
},
"relationships": {
"downloads": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002229/downloads?format=api"
}
},
"geocoordinates": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002229/geocoordinates?format=api"
}
},
"analyses": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002229/analyses?format=api"
}
},
"biomes": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002229/biomes?format=api"
},
"data": [
{
"type": "biomes",
"id": "root:Host-associated:Human:Digestive system:Oral:Subgingival plaque",
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Host-associated:Human:Digestive%20system:Oral:Subgingival%20plaque?format=api"
}
}
]
},
"publications": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002229/publications?format=api"
}
},
"samples": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002229/samples?format=api"
}
}
},
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002229?format=api"
}
},
{
"type": "studies",
"id": "MGYS00002224",
"attributes": {
"accession": "MGYS00002224",
"bioproject": "PRJNA324274",
"samples-count": 101,
"is-private": false,
"last-update": "2019-11-07T16:55:42",
"secondary-accession": "SRP077982",
"centre-name": "Universidade de Sao Paulo",
"public-release-date": null,
"study-abstract": "The present study aims to evaluate the composition of the subgingival plaque community associated with periodontal health and disease using high throughput sequencing approaches",
"study-name": "human oral metagenome Raw sequence reads",
"data-origination": "HARVESTED"
},
"relationships": {
"downloads": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002224/downloads?format=api"
}
},
"geocoordinates": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002224/geocoordinates?format=api"
}
},
"analyses": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002224/analyses?format=api"
}
},
"biomes": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002224/biomes?format=api"
},
"data": [
{
"type": "biomes",
"id": "root:Host-associated:Human:Digestive system:Oral:Subgingival plaque",
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Host-associated:Human:Digestive%20system:Oral:Subgingival%20plaque?format=api"
}
}
]
},
"publications": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002224/publications?format=api"
}
},
"samples": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002224/samples?format=api"
}
}
},
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002224?format=api"
}
},
{
"type": "studies",
"id": "MGYS00002173",
"attributes": {
"accession": "MGYS00002173",
"bioproject": "PRJNA274944",
"samples-count": 224,
"is-private": false,
"last-update": "2019-11-07T16:55:40",
"secondary-accession": "SRP060310",
"centre-name": "National Tsing Hua University",
"public-release-date": null,
"study-abstract": "Subgingival samples from Healthy / Periodontitis subjects",
"study-name": "Subgingival samples from Healthy / Periodontitis subjects Targeted Locus (Loci)",
"data-origination": "HARVESTED"
},
"relationships": {
"downloads": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002173/downloads?format=api"
}
},
"geocoordinates": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002173/geocoordinates?format=api"
}
},
"analyses": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002173/analyses?format=api"
}
},
"biomes": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002173/biomes?format=api"
},
"data": [
{
"type": "biomes",
"id": "root:Host-associated:Human:Digestive system:Oral:Subgingival plaque",
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Host-associated:Human:Digestive%20system:Oral:Subgingival%20plaque?format=api"
}
}
]
},
"publications": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002173/publications?format=api"
}
},
"samples": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002173/samples?format=api"
}
}
},
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002173?format=api"
}
},
{
"type": "studies",
"id": "MGYS00001300",
"attributes": {
"accession": "MGYS00001300",
"bioproject": "PRJNA239461",
"samples-count": 14,
"is-private": false,
"last-update": "2019-11-07T16:55:38",
"secondary-accession": "SRP038999",
"centre-name": "University of Connecticut",
"public-release-date": null,
"study-abstract": "Background and Objective: The advent of next-generation sequencing has significantly facilitated characterization of the oral microbiome. Despite great efforts in streamlining the processes of sequencing and data curation, upstream steps required for amplicon library generation could still influence 16S rRNA gene-based microbial profiles. Among upstream processes, DNA extraction is a critical step that could represent a great source of bias. Accounting for bias introduced by extraction procedures is important when comparing studies that use different methods. Identifying the method that best portrays communities is also desirable. Accordingly, the aim of this study was to evaluate bias introduced by different DNA extraction procedures on oral microbiome profiles. Design: Four DNA extraction methods were tested on mock communities consisting of seven representative oral bacteria. Additionally, supragingival plaque samples were collected from 7 individuals and divided equally to test two commonly used DNA extraction procedures. Amplicon libraries of the 16S rRNA gene were generated and sequenced via 454-pyrosequencing. Results: Evaluation of mock communities revealed that DNA yield and bacterial species representation varied with DNA extraction method. Despite producing the lowest yield of DNA, a method that included bead beating was the only protocol able to detect all seven species in the mock community. Comparison of the performance of two commonly used methods (crude lysis and a chemical/enzymatic lysis + column-based DNA isolation) on plaque samples showed no effect of extraction protocols on taxa prevalence but global community structure and relative abundance of individual taxa were affected. At the phylum level, the latter method improved the recovery of Actinobacteria, Bacteroidetes and Spirochaetes over crude lysis. Conclusion: DNA extraction distorts microbial profiles in simulated and clinical oral samples, reinforcing the importance of careful selection of a DNA extraction protocol to improve species recovery and facilitate data comparison across oral microbiology studies.",
"study-name": "Influence of DNA extraction on oral microbial profiles obtained via 16S rRNA gene sequencing- Supragingival plaque",
"data-origination": "HARVESTED"
},
"relationships": {
"downloads": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00001300/downloads?format=api"
}
},
"geocoordinates": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00001300/geocoordinates?format=api"
}
},
"analyses": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00001300/analyses?format=api"
}
},
"biomes": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00001300/biomes?format=api"
},
"data": [
{
"type": "biomes",
"id": "root:Host-associated:Human:Digestive system:Oral:Subgingival plaque",
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Host-associated:Human:Digestive%20system:Oral:Subgingival%20plaque?format=api"
}
}
]
},
"publications": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00001300/publications?format=api"
}
},
"samples": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00001300/samples?format=api"
}
}
},
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00001300?format=api"
}
},
{
"type": "studies",
"id": "MGYS00002358",
"attributes": {
"accession": "MGYS00002358",
"bioproject": "PRJDB4192",
"samples-count": 44,
"is-private": false,
"last-update": "2018-04-26T09:53:43",
"secondary-accession": "DRP003845",
"centre-name": "KYOTO_GM",
"public-release-date": null,
"study-abstract": "Eleven patients who have peri-implantitis and periodontitis were selected. They were evaluated based on the clinical examination and radiographic data. Sub-gingival and sub-mucosal biofilm samples were taken from the deepest pockets of each site, and we characterized bacterial community of 16S rRNA and 16S rRNA genes (rDNA) using Illumina miseq.",
"study-name": "Core function of microbiota in peri-implantitis and periodontitis",
"data-origination": "HARVESTED"
},
"relationships": {
"downloads": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002358/downloads?format=api"
}
},
"geocoordinates": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002358/geocoordinates?format=api"
}
},
"analyses": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002358/analyses?format=api"
}
},
"biomes": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002358/biomes?format=api"
},
"data": [
{
"type": "biomes",
"id": "root:Host-associated:Human:Digestive system:Oral:Subgingival plaque",
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Host-associated:Human:Digestive%20system:Oral:Subgingival%20plaque?format=api"
}
}
]
},
"publications": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002358/publications?format=api"
}
},
"samples": {
"links": {
"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002358/samples?format=api"
}
}
},
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002358?format=api"
}
}
],
"meta": {
"pagination": {
"page": 1,
"pages": 1,
"count": 18
}
}
}