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                "study-abstract": "A metagenomic study, using 16S amplicon approach, has been performed to analyze bacterial communities of compost tea, teku kana and litter used to produce it.",
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                "study-abstract": "The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA230567, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Engineered:Wastewater.",
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                "study-abstract": "This study aimed to evaluate the long-term operation of an up-flow anaerobic packed bed reactor (APBR) filled with low-density of polyethylene (LDP) and applied to thermophilic hydrogen production using sugarcane vinasse as substrate. The APBR was operated at organic loading rate (OLR) of 84.2 kg-COD.m-3.d-1, value determined in earlier study. The maximum values of hydrogen production and yield were 5,252.6 mL-H2.d-1 and 3.7 mol-H2.mol-1total carbohydrates, respectively. However, as the OLR applied was constant, the values of specific organic load rate (sOLR) decreased throughout operation from values from 1.38 to 0.72 g-Total carbohydrates.g-VS-1.h-1, thus, interfering negatively on hydrogen production. sOLR values around 1.22 g-Total carbohydrates.g-VS-1.h-1 indicated optimal conditions for hydrogen production. The microbial community was study by 454-pyrosequencing analysis. Organisms belonging to genera Caloramotor, Clostridium, Thermoanaerobacterium, Thermohydrogenium, Caldanaerobius and Megasphaera were detected in samples taken from reactor at days 30 and 60 of operation, suggesting a role in the hydrogen production.",
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                "geocoordinates": {
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                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002659/analyses?format=api"
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                },
                "samples": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002659/samples?format=api"
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                "biomes": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002659/biomes?format=api"
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                    "data": [
                        {
                            "type": "biomes",
                            "id": "root:Engineered:Solid waste",
                            "links": {
                                "self": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Engineered:Solid%20waste?format=api"
                            }
                        }
                    ]
                }
            },
            "links": {
                "self": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002659?format=api"
            }
        },
        {
            "type": "studies",
            "id": "MGYS00001561",
            "attributes": {
                "bioproject": "PRJEB6513",
                "samples-count": 71,
                "accession": "MGYS00001561",
                "is-private": false,
                "last-update": "2024-01-23T14:02:35",
                "secondary-accession": "ERP006054",
                "centre-name": "King Abdullah University of Science and Technology (KAUST)",
                "public-release-date": null,
                "study-abstract": "In this study, 16S rRNA gene pyrosequencing was applied in order to provide a better insight on the effect of solids retention time (SRT) on the diversity and dynamics of total, dominant and rare bacterial taxa in eight replicate lab-scale sequencing batch reactors (SBRs) operated for a period of 78 days and seeded with either acclimated or non-acclimated sludge. Rank-abundance curves showed strong abundance of few dominant operational taxonomic units (OTUs) and a long tail of rare OTUs in all reactors. Results revealed that there was no detectable effect of SRT (2d vs. 10d) on Shannon diversity index and OTU richness of both dominant and rate taxa. Nonmetric Multidimensional Scaling (NMDS) analysis showed that the total, dominant and rare bacterial taxa were highly dynamic during entire period of stable reactor performance. Also, the rare taxa were more dynamic than the dominant taxa despite expected low invasion rates because of the use of sterile synthetic media. Moving-window analysis, Global ANOSIM and NMDS analysis revealed that the bacterial community structure in replicate SBRs seeded with acclimated or non-acclimated sludge was reproducible. Overall 16S rRNA gene pyrosequencing could reveal the dynamics of rare bacterial taxa that are normally left out using conventional molecular biology methods.",
                "study-name": "Diversity and dynamics of dominant and rare bacterial taxa in replicate sequencing batch reactors operated under different solids retention time and seeded with either acclimated or non-acclimated sludge",
                "data-origination": "SUBMITTED"
            },
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                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00001561/analyses?format=api"
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                "samples": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00001561/samples?format=api"
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                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00001561/biomes?format=api"
                    },
                    "data": [
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                            "type": "biomes",
                            "id": "root:Engineered:Bioreactor:Continuous culture",
                            "links": {
                                "self": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Engineered:Bioreactor:Continuous%20culture?format=api"
                            }
                        }
                    ]
                }
            },
            "links": {
                "self": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00001561?format=api"
            }
        },
        {
            "type": "studies",
            "id": "MGYS00006558",
            "attributes": {
                "bioproject": "PRJNA230567",
                "samples-count": 89,
                "accession": "MGYS00006558",
                "is-private": false,
                "last-update": "2023-12-19T12:35:08",
                "secondary-accession": "SRP033648",
                "centre-name": "Luxembourg Centre for Systems Biomedicine",
                "public-release-date": null,
                "study-abstract": "Characterization of microbial communities at the genomic, transcriptomic, proteomic and metabolomic levels, with a special interest on lipid accumulating bacterial populations, which are naturally enriched in biological wastewater treatment systems and may be harnessed for the conversion of mixed lipid substrates (wastewater) into biodiesel. The project aims to elucidate the genetic blueprints and the functional relevance of specific populations within the community. It focuses on within-population genetic and functional heterogeneity, trying to understand how fine-scale variations contribute to differing lipid accumulating phenotypes. Insights from this project will contribute to the understanding the functioning of microbial ecosystems, and improve optimization and modeling strategies for current and future biological wastewater treatment processes.  This BioProject contains datasets derived from the same biological wastewater treatment plant. The date includes metagenomes, metatranscriptomes and organisms isolated in pure cultures.",
                "study-name": "Systems Biology of Lipid Accumulating Organisms",
                "data-origination": "HARVESTED"
            },
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                },
                "publications": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006558/publications?format=api"
                    }
                },
                "geocoordinates": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006558/geocoordinates?format=api"
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                "analyses": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006558/analyses?format=api"
                    }
                },
                "samples": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006558/samples?format=api"
                    }
                },
                "biomes": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006558/biomes?format=api"
                    },
                    "data": [
                        {
                            "type": "biomes",
                            "id": "root:Engineered:Wastewater",
                            "links": {
                                "self": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Engineered:Wastewater?format=api"
                            }
                        }
                    ]
                }
            },
            "links": {
                "self": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006558?format=api"
            }
        },
        {
            "type": "studies",
            "id": "MGYS00006492",
            "attributes": {
                "bioproject": "PRJNA889035",
                "samples-count": 36,
                "accession": "MGYS00006492",
                "is-private": false,
                "last-update": "2023-09-20T19:31:43",
                "secondary-accession": "SRP402102",
                "centre-name": "Midwestern University",
                "public-release-date": null,
                "study-abstract": "Various surfaces of a physical therapy gym were sampled using swabs, which were then subject to 16S rRNA analysis in order to describe how the microbiome changes according to porosity, contact frequency, cleaning frequency, and physical location within the environment.",
                "study-name": "Variation in the microbiome on the surfaces of a physical therapy gym",
                "data-origination": "HARVESTED"
            },
            "relationships": {
                "downloads": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006492/downloads?format=api"
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                },
                "publications": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006492/publications?format=api"
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                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006492/geocoordinates?format=api"
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                "analyses": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006492/analyses?format=api"
                    }
                },
                "samples": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006492/samples?format=api"
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                },
                "biomes": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006492/biomes?format=api"
                    },
                    "data": [
                        {
                            "type": "biomes",
                            "id": "root:Engineered:Built environment",
                            "links": {
                                "self": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Engineered:Built%20environment?format=api"
                            }
                        }
                    ]
                }
            },
            "links": {
                "self": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006492?format=api"
            }
        },
        {
            "type": "studies",
            "id": "MGYS00001361",
            "attributes": {
                "bioproject": "PRJEB8282",
                "samples-count": 107,
                "accession": "MGYS00001361",
                "is-private": false,
                "last-update": "2023-09-20T13:36:15",
                "secondary-accession": "ERP009341",
                "centre-name": "Natural Resources Institute Finland (Luke)",
                "public-release-date": null,
                "study-abstract": "Modern molecular techniques provide a comprehensive and high-resolution window into complex systems that are difficult to study with traditional macroscopic techniques. We applied culture-free DNA extraction and 454-pyrosequencing to study the fungal microflora of decaying Norway spruce (Picea abies [L.] Karst.) logs in five unmanaged boreal forests. Fungal diversity and wood density were inversely related, i.e., OTU richness generally increased as the log became increasingly decomposed. According to generalized additive mixed models white-rot fungi (e.g., Phellinus nigrolimitatus) and members of Hyphodontia did not show a clear response to the wood-density gradient, whereas Phellinus viticola and brown-rot fungi (e.g., Fomitopsis pinicola, Antrodia serialis, Coniophora olivaceae) peaked during intermediate decay and mycorrhizal fungi (e.g., Piloderma, Tylospora, Russula) increased in the later stages. This information on fungal habitat requirements facilitates development of management practices that preserve fungal diversity in managed forests.",
                "study-name": "Habitat models of wood-inhabiting fungi along a decay gradient of Norway spruce logs",
                "data-origination": "SUBMITTED"
            },
            "relationships": {
                "downloads": {
                    "links": {
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                },
                "publications": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00001361/publications?format=api"
                    }
                },
                "geocoordinates": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00001361/geocoordinates?format=api"
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                },
                "analyses": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00001361/analyses?format=api"
                    }
                },
                "samples": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00001361/samples?format=api"
                    }
                },
                "biomes": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00001361/biomes?format=api"
                    },
                    "data": [
                        {
                            "type": "biomes",
                            "id": "root:Engineered:Solid waste:Composting:Wood",
                            "links": {
                                "self": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Engineered:Solid%20waste:Composting:Wood?format=api"
                            }
                        }
                    ]
                }
            },
            "links": {
                "self": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00001361?format=api"
            }
        },
        {
            "type": "studies",
            "id": "MGYS00006097",
            "attributes": {
                "bioproject": "PRJEB58160",
                "samples-count": 12,
                "accession": "MGYS00006097",
                "is-private": false,
                "last-update": "2023-03-23T17:24:24",
                "secondary-accession": "ERP143223",
                "centre-name": "Arcadia Science",
                "public-release-date": null,
                "study-abstract": "We used short and long read metagenomics to look at the microbial diversity of cheese rind biofilms from several washed rind cheeses. Short reads were assembled with metaSPAdes 3.15.3. Oxford Nanopore reads were assembled with metaFlye 2.9.1 and polished with medaka 1.7.2. The following samples were sequenced with both Illumina and Oxford Nanopore Technologies and are samples from the same style of cheese sampled at different times throughout the aging process (early, middle, and late timepoints spanning the standard aging time for each cheese style):\nEL2W, EL4W, EL12W (2, 4, 12 weeks)\nOM2W, OM4W, OM8W (2, 4, 8 weeks)\nWH1M, WH2M, WH4M (1, 2, 4 months)",
                "study-name": "Metagenomics of Washed Rind Cheese Communities",
                "data-origination": "SUBMITTED"
            },
            "relationships": {
                "downloads": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006097/downloads?format=api"
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                },
                "publications": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006097/publications?format=api"
                    }
                },
                "geocoordinates": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006097/geocoordinates?format=api"
                    }
                },
                "analyses": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006097/analyses?format=api"
                    }
                },
                "samples": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006097/samples?format=api"
                    }
                },
                "biomes": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006097/biomes?format=api"
                    },
                    "data": [
                        {
                            "type": "biomes",
                            "id": "root:Engineered:Food production:Dairy products",
                            "links": {
                                "self": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Engineered:Food%20production:Dairy%20products?format=api"
                            }
                        }
                    ]
                }
            },
            "links": {
                "self": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006097?format=api"
            }
        },
        {
            "type": "studies",
            "id": "MGYS00006110",
            "attributes": {
                "bioproject": "PRJNA314466",
                "samples-count": 91,
                "accession": "MGYS00006110",
                "is-private": false,
                "last-update": "2023-02-22T19:07:01",
                "secondary-accession": "SRP071345",
                "centre-name": "INRA",
                "public-release-date": null,
                "study-abstract": "",
                "study-name": "16S-based metagenomic study of twelve French cheese varieties",
                "data-origination": "HARVESTED"
            },
            "relationships": {
                "downloads": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006110/downloads?format=api"
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                },
                "publications": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006110/publications?format=api"
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                },
                "geocoordinates": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006110/geocoordinates?format=api"
                    }
                },
                "analyses": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006110/analyses?format=api"
                    }
                },
                "samples": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006110/samples?format=api"
                    }
                },
                "biomes": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006110/biomes?format=api"
                    },
                    "data": [
                        {
                            "type": "biomes",
                            "id": "root:Engineered:Food production:Dairy products",
                            "links": {
                                "self": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Engineered:Food%20production:Dairy%20products?format=api"
                            }
                        }
                    ]
                }
            },
            "links": {
                "self": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006110?format=api"
            }
        },
        {
            "type": "studies",
            "id": "MGYS00006036",
            "attributes": {
                "bioproject": "PRJEB52176",
                "samples-count": 1,
                "accession": "MGYS00006036",
                "is-private": false,
                "last-update": "2022-07-24T14:59:37",
                "secondary-accession": "ERP136868",
                "centre-name": "Department of Biosciences and Bioengineering",
                "public-release-date": null,
                "study-abstract": "Compost is an aerobic self-heating environment that houses biological degraders capable of degrading wood, starch, cellulose, lignin, lipids, peptides and other carbohydrates. It has cycle of thermophilic heating and cooling phases due to oxidation of the organic matter into inorganic matter until the maturation where it will be used as a fertilizer. Compost attracts attention as it is readily accessible hotspot for thermophilic microorganisms and its enzymes. The enzymes such as amylases, cellulases, proteases and lipases are being sought in industries and are being replaced with its mesophilic counterparts. Metagenome of manure compost was isolated and sequenced. It revealed abundances of Actinobacteria, proteobacteria, fermicutes lineages",
                "study-name": "Cattle manure compost metagenome as a source of industrially important enzymes",
                "data-origination": "SUBMITTED"
            },
            "relationships": {
                "downloads": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006036/downloads?format=api"
                    }
                },
                "publications": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006036/publications?format=api"
                    }
                },
                "geocoordinates": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006036/geocoordinates?format=api"
                    }
                },
                "analyses": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006036/analyses?format=api"
                    }
                },
                "samples": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006036/samples?format=api"
                    }
                },
                "biomes": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006036/biomes?format=api"
                    },
                    "data": [
                        {
                            "type": "biomes",
                            "id": "root:Engineered:Solid waste:Composting",
                            "links": {
                                "self": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Engineered:Solid%20waste:Composting?format=api"
                            }
                        }
                    ]
                }
            },
            "links": {
                "self": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006036?format=api"
            }
        },
        {
            "type": "studies",
            "id": "MGYS00006025",
            "attributes": {
                "bioproject": "PRJNA259818",
                "samples-count": 1,
                "accession": "MGYS00006025",
                "is-private": false,
                "last-update": "2022-06-06T14:12:30",
                "secondary-accession": "SRP045926",
                "centre-name": "Nelson Mandela African Institution of Sciences and Technology",
                "public-release-date": null,
                "study-abstract": "Following increase in population size, urbanization and human activities, there is poor solid waste management in urban and peri-urban areas, mostly in Sub Sahara Africa. Varieties of solid wastes such as medical waste, domestic waste and industrial waste along with their associated microbes are dumped at the same place. We are witnessing high interaction between wild and domestic animals as well as people in municipal dumps. We hypothesized the municipal dumps to be the driver for the emergence of new pathogens of public health importance. We wanted to know the abundance, diversity and dynamics of bacteria circulating in municipal dumpsite and the associated risks. This knowledge is key towards improved solid waste management, hence mitigation of the associated risks.",
                "study-name": "Municipal Solid wastes Metagenome",
                "data-origination": "HARVESTED"
            },
            "relationships": {
                "downloads": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006025/downloads?format=api"
                    }
                },
                "publications": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006025/publications?format=api"
                    }
                },
                "geocoordinates": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006025/geocoordinates?format=api"
                    }
                },
                "analyses": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006025/analyses?format=api"
                    }
                },
                "samples": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006025/samples?format=api"
                    }
                },
                "biomes": {
                    "links": {
                        "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006025/biomes?format=api"
                    },
                    "data": [
                        {
                            "type": "biomes",
                            "id": "root:Engineered:Solid waste",
                            "links": {
                                "self": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Engineered:Solid%20waste?format=api"
                            }
                        }
                    ]
                }
            },
            "links": {
                "self": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00006025?format=api"
            }
        },
        {
            "type": "studies",
            "id": "MGYS00006002",
            "attributes": {
                "bioproject": "PRJEB51134",
                "samples-count": 6,
                "accession": "MGYS00006002",
                "is-private": false,
                "last-update": "2022-03-17T09:53:09",
                "secondary-accession": "ERP135733",
                "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 PRJEB24129, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Engineered:Food production:Fermented beverages.",
                "study-name": "EMG produced TPA metagenomics assembly of PRJEB24129 data set (Temporal shotgun metagenomic dissection of the coffee fermentation ecosystem).",
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