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"centre-name": "EMG",
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"study-abstract": "The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA435487, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Birds:Digestive system:Digestive tube:Cecum.",
"study-name": "EMG produced TPA metagenomics assembly of PRJNA435487 data set (Chicken ceacal metagenome).",
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"bioproject": "PRJEB33036",
"accession": "MGYS00005623",
"is-private": false,
"last-update": "2020-10-13T16:51:05",
"secondary-accession": "ERP115793",
"centre-name": "Quadram Institute Bioscience",
"public-release-date": null,
"study-abstract": "16S rRNA amplicon sequencing of broiler caecal contents. Linked to this study: https://doi.org/10.1186/s42523-019-0015-1",
"study-name": "16S rRNA amplicon sequencing of broiler caecal contents",
"data-origination": "SUBMITTED"
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"accession": "MGYS00005593",
"is-private": false,
"last-update": "2020-08-24T18:22:50",
"secondary-accession": "ERP111337",
"centre-name": "NEIKER-Instituto Vasco de Investigacion y Desarrollo Agrario",
"public-release-date": null,
"study-abstract": "Gut microbiota affects health, metabolism and immunity of the host, and in the case of livestock,\nalso food-safety. Here, 16S rRNA gene high-throughput Illumina sequencing was used to describe the\nmicrobiome of chicken caeca in two different breeds and management systems throughout their whole\nproductive lifespan. Broilers (Ross-308), as a fast-growing breed reared in an intensive system for 42-\ndays, and a slow-growing breed of chicken (Sasso-T451A) reared in an extensive farming system with\noutdoor access for 86-days, were compared. The core microbiome and differentially abundant taxa,\nas well as taxa associated with age were identified. Age was identified as the strongest influencing\nfactor in caecal microbiota composition, and, in general, each age-group showed an age-associated\ncommunity profile, with a transition period at the middle of their lifespan. However, substantial\ndifferences were observed in the composition of caecal microbiota of both chicken breeds, microbiota\nbeing richer and more complex in free-range chicken than in broilers. Several taxa positively/negatively\ncorrelated with Campylobacter relative abundance were also identified. Especially noteworthy was\nthe identification by microbial community comparison of microbiota profiles suggestive of dysbiosis in\nseveral free-range chickens, probably associated to the typhlitis observed in the lumen of their caeca.",
"study-name": "16S rRNA amplicon sequencing characterization of caecal microbiome composition of broilers and free-range slow-growing chickens throughout their productive lifespan",
"data-origination": "SUBMITTED"
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"bioproject": "PRJNA299358",
"accession": "MGYS00005542",
"is-private": false,
"last-update": "2020-06-29T15:10:47",
"secondary-accession": "SRP065093",
"centre-name": "Sichuan university",
"public-release-date": null,
"study-abstract": "To reveal the bacteria community related to Tibetan Chicken caecum",
"study-name": "Tibetan Chicken caecum feces Targeted Locus (Loci)",
"data-origination": "HARVESTED"
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"bioproject": "PRJEB24821",
"accession": "MGYS00002686",
"is-private": false,
"last-update": "2020-05-18T01:05:40",
"secondary-accession": "ERP106676",
"centre-name": "EMBL-EBI",
"public-release-date": null,
"study-abstract": "The Colonization and Succession of Hospital-Associated Microbiota Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB13117. This project includes samples from the following biomes: Engineered,Built environment.",
"study-name": "EMG produced TPA metagenomics assembly of the Hospital Metagenomics (Colonization and Succession of Hospital-Associated Microbiota) data set.",
"data-origination": "SUBMITTED"
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"last-update": "2019-11-07T16:52:10",
"secondary-accession": "SRP019776",
"centre-name": "Birmingham University",
"public-release-date": null,
"study-abstract": "Chickens are major source of food and protein worldwide. Feed conversion and the health of chickens relies on the largely unexplored complex microbial community that inhabits the chicken gut, particularly the ceca. Therefore a studly goal was to use in-depth metagenomics of the ceca to examine the microbial community from the ceca of a Broiler Chicken.",
"study-name": "Chicken cecal contents Metagenome",
"data-origination": "HARVESTED"
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"last-update": "2017-11-16T13:22:04",
"secondary-accession": "ERP105105",
"centre-name": "ANAND",
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"study-abstract": "There is rich genetic diversity in India's native poultry breeds, and the hybrid exotic lines often used in Indian commercial production are distinct from the majority of poultry reared in the UK. The prevalence and dynamics of gastrointestinal infection at farm-level has a direct bearing on economic risk to individual farmers and contributes to overall global concerns of food security and food safety.Changes to diet, use of vaccines or antimicrobials, and flock-level interventions such as ‘thinning', can have profound effects on intestinal health and the evolution and spread of disease-causing microbes and may be amplified by genetic variation in host and microbe populations. Whilst major advances in genomics and genotyping of commercial poultry lines is facilitating the identification of loci linked to susceptibility or resistance, the impact of host and pathogen diversity on disease and production outcomes remains largely unexplored.",
"study-name": "BBSRC Main Experiment Shotgun Study",
"data-origination": "SUBMITTED"
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"bioproject": "PRJEB17637",
"accession": "MGYS00001311",
"is-private": false,
"last-update": "2016-11-21T10:58:48",
"secondary-accession": "ERP019507",
"centre-name": "LSA-DISTAL-UNIBO",
"public-release-date": null,
"study-abstract": "Impact of LAB supplementation in drinking water on chicken crop and ceca tested at 14 and 35 days",
"study-name": "Impact of LAB supplementation in drinking water on chicken crop and ceca",
"data-origination": "SUBMITTED"
},
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"is-private": false,
"last-update": "2016-11-18T11:43:46",
"secondary-accession": "ERP018631",
"centre-name": "DISTAL (University of Bologna)",
"public-release-date": null,
"study-abstract": "Metagenomic study of cecum contents of chickens fed with LAB",
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