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{
"type": "studies",
"id": "MGYS00005631",
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"bioproject": "PRJEB40874",
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"is-private": false,
"last-update": "2020-11-04T16:04:48",
"secondary-accession": "ERP124570",
"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 PRJEB14491, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Birds:Digestive system:Digestive tube:Cecum.",
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{
"type": "studies",
"id": "MGYS00005623",
"attributes": {
"accession": "MGYS00005623",
"bioproject": "PRJEB33036",
"samples-count": 11,
"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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},
{
"type": "studies",
"id": "MGYS00005621",
"attributes": {
"accession": "MGYS00005621",
"bioproject": "PRJNA517082",
"samples-count": 60,
"is-private": false,
"last-update": "2020-10-12T16:55:12",
"secondary-accession": "SRP182090",
"centre-name": "Wageningen University and Research",
"public-release-date": null,
"study-abstract": "The fine-scale temporal dynamics of the chicken gut microbiome are unexplored, but thought to be critical for chicken health and productivity. Here, we monitored the fecal microbiome of healthy chickens on days 1-7, 10, 14, 21, 28, and 35 after hatching, and performed 16S rRNA amplicon sequencing in order to obtain a high-resolution census of the fecal microbiome over time. In the period studied, the fecal microbiomes of the developing chickens showed a linear-log increase in community richness and consistent shifts in community composition. Three successional stages were detected: the first stage was dominated by vertically-transmitted or rapidly-colonizing taxa including Streptococcus and Escherichia/Shigella; in the second stage beginning on day 4, these taxa were displaced by rapid-growing taxa including Lachnospiraceae and Ruminococcus-like SVs; and in the third stage, starting on day 10, slow-growing, specialist taxa including Candidatus Arthrobacter and Romboutsia were detected. The patterns of displacement and the previously reported ecological characteristics of many of the dominant taxa observed suggest that resource competition plays an important role in regulating successional dynamics in the developing chicken gut. We propose that the boundaries between successional stages (3-4 and 14-21 days after hatching) may be optimal times for microbiome interventions.",
"study-name": "Patterns of community assembly in the developing chicken microbiome reveal rapid primary succession",
"data-origination": "HARVESTED"
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"data": [
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"type": "biomes",
"id": "root:Host-associated:Birds:Digestive system:Fecal",
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Host-associated:Birds:Digestive%20system:Fecal?format=api"
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{
"type": "studies",
"id": "MGYS00005611",
"attributes": {
"accession": "MGYS00005611",
"bioproject": "PRJNA611508",
"samples-count": 117,
"is-private": false,
"last-update": "2020-09-24T01:51:48",
"secondary-accession": "SRP252220",
"centre-name": "INRAE",
"public-release-date": null,
"study-abstract": "Microbiota characterization of caecal, ileum, and jejunal contents of two lines of broiler chickens divergently selected on their digestive efficiency",
"study-name": "Galmide",
"data-origination": "HARVESTED"
},
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"related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00005611/biomes?format=api"
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"data": [
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"type": "biomes",
"id": "root:Host-associated:Birds:Digestive system",
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Host-associated:Birds:Digestive%20system?format=api"
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},
{
"type": "studies",
"id": "MGYS00005610",
"attributes": {
"accession": "MGYS00005610",
"bioproject": "PRJEB25776",
"samples-count": 251,
"is-private": false,
"last-update": "2020-09-23T23:14:55",
"secondary-accession": "ERP107730",
"centre-name": "LSHTM",
"public-release-date": null,
"study-abstract": "Chickens are a key food source for humans yet their microbiome contains bacteria that can be pathogenic to humans, and indeed potentially to chickens themselves. Campylobacter is present within the chicken gut and is the leading cause of bacterial foodborne gastroenteritis within humans worldwide. Infection can lead to secondary sequelae such as Guillain-Barre syndrome and stunted growth in children from low-resource areas. Despite the global health impact and economic burden of Campylobacter, how and when Campylobacter appears within chickens remains unclear. The lack of day to day microbiome data with replicates, relevant metadata, and a lack of natural infection studies have delayed our understanding of the chicken gut microbiome and Campylobacter. Here, we performed a comprehensive day to day microbiome analysis of the chicken cecum from day 3 to 35 (12 replicates each day; final n = 379). We combined metadata such as chicken weight and feed conversion rates to investigate what the driving forces are for the microbial changes within the chicken gut over time, and how this relates to Campylobacter appearance within a natural habitat setting. We found a rapidly increasing microbial diversity up to day 12 with variation observed both in terms of genera and abundance, before a stabilization of the microbial diversity after day 20. In particular, we identified a shift from competitive to environmental drivers of microbial community from days 12 to 20 creating a window of opportunity whereby Campylobacter can appear. Campylobacter was identified at day 16 which was 1 day after the most substantial changes in metabolic profiles observed. In addition, microbial variation over time is most likely influenced by the diet of the chickens whereby significant shifts in OTU abundances and beta dispersion of samples often corresponded with changes in feed. This study is unique in comparison to the most recent studies as neither sampling was sporadic nor Campylobacter was artificially introduced, thus the experiments were performed in a natural setting. We believe that our findings can be useful for future intervention strategies and help reduce the burden of Campylobacter within the food chain.",
"study-name": "Comprehensive longitudinal microbiome analysis of the chicken cecum reveals a shift from competitive to environmental drivers and a window of opportunity for Campylobacter",
"data-origination": "SUBMITTED"
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"pages": 3,
"count": 59
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}