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"study-abstract": "Samples of litter were collected from poultry houses to examine the litter bacterial microbiome and how this changes during the production cycle. Samples were collected from six farms which used a variety of bedding types. Samples were collected for two consecutive production cycles from each farm during the early, middle and late parts of the cycle. Litter samples were transported to the laboratory on ice and thoroughly mixed with sterile phosphate buffered saline (PBS) at a 1:1 ratio (vol:vol). Aliquots of the PBS were frozen until DNA was extracted using Qiagen Powersoil Pro kit (according to manufacturers instructions). The v4 region of the 16s rRNA gene was sequenced using an Illumina Miseq (250bp paired end reads).",
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"last-update": "2017-06-08T09:06:46",
"secondary-accession": "ERP023305",
"centre-name": "LSA-DISTAL-UNIBO",
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"study-abstract": "Poultry feces have been spiked with known concentration of bacteria and stored at different times and temperatures before DNA extraction",
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"id": "MGYS00001735",
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"last-update": "2017-05-08T13:35:17",
"secondary-accession": "ERP022776",
"centre-name": "NORWEGIAN VETERINARY INSTITUTE",
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"study-abstract": "Conventional rearing of broiler chickens is based on routine supplementation of the feed with anticoccidials which are approved for use against intestinal coccidiosis. A sub-group of anticoccidials, which functions as ionophores, is also effective against some gram-positive bacteria, including Clostridium perfringens. This is an intestinal bacterium associated with growth depression and important gastrointestinal health problems such as necrotic enteritis and the gizzard erosion syndrome. The dual function of ionophores is part of the explanation to their widespread use in broiler feeds. The ionophore narasin has been the predominant anticoccidial used in broiler rearing in the Nordic countries. Research suggests that although narasin is not used in human medicine, its use in broiler rearing might promote persistence of vancomycin resistant enterococci. This has led to an expressed concern that use of narasin may stimulate occurrence and spread of bacteria resistant to clinically relevant antibiotics. Dissemination of antibiotic resistant bacteria is a world-wide problem, and there is an increasing pressure to reduce the use of antimicrobial agents in animal production. The purpose of this project was to test non-antibiotic feed additives and identify characteristics of the intestinal microbiota in chickens fed diets supplemented with these alternatives to in-feed anticoccidials.The samples originate from four different feeding trials with Ross 308 broiler chickens reared under similar conditions. The chickens were divided into 6 groups, which were fed similar commercial pelleted diets formulated to meet the Ross 308 nutrition specifications with group specific supplements.Trial 1: group 1, narasin; group 2, no additive; group 3, acid product-A; group 4, acid product-B; group 5, acid product-C; group 6, acid product-D.Trial 2: group 1, narasin; group 2, no additive; group 3, acid product-E; group 4, acid product-F, group 5; yeast product-A, group 6; plant/acid product-A.Trial 3: group 1, narasin; group 2, no additive; group 3; yeast product-B + synbiotic-A, group 4; yeast product-B + plant product-A; group 5, yeast product-A + acid product-B; group 6, yeast product-A + acid product-D.Trial 4: group 1, narasin; group 2, no additive",
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"id": "MGYS00001723",
"attributes": {
"bioproject": "PRJEB20586",
"samples-count": 8,
"accession": "MGYS00001723",
"is-private": false,
"last-update": "2017-05-02T11:30:24",
"secondary-accession": "ERP022755",
"centre-name": "KYOTO UNIVERSITY",
"public-release-date": null,
"study-abstract": "Metagenomic analysis of chicken cecal feces obtained from chicken farm in Japan were carried out to know microbiota composition.",
"study-name": "Metagenomic analysis of chicken cecal feces",
"data-origination": "SUBMITTED"
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"id": "MGYS00001698",
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"bioproject": "PRJEB20194",
"samples-count": 28,
"accession": "MGYS00001698",
"is-private": false,
"last-update": "2017-04-19T16:50:17",
"secondary-accession": "ERP022330",
"centre-name": "ANAND",
"public-release-date": null,
"study-abstract": "World population leading to consequent high pressure placed on animal biotechnologists/ researcher to increase the yield of current food crops and livestock, while identifying new and alternative food sources. In today's economically fast growing world poultry industry is also feeling its pace to be increased. Identification of genes associated with fatness or leanness will help in selection of individuals with better performance and thereby results in profitable poultry farming. In addition, Whole transcriptome shotgun sequencing or RNA-seq is an efficient and reliable technology for transcriptomic analysis so as to reveal genetic architecture, to identify sequence variation, and to quantify gene expression. The ultimate aim is to identify the genes which are associated with feed conversion ratio. The biomarkers identified will be useful for selection of birds with low FCR. The host genetic responses associated with weight gain and feed conversion efficiency have also played a role in changes in the physiology and gut microbial structure of birds. Therefore, shot gun and amplicon sequencing will be carrying out of each metagenomes. The ultimate aim is to detect possible association between FCR and gut microflora. The bacteria identified could be useful for feed formulation for broiler. Successful completion of project will result in identification of novel/ unigene associated with FCR in broiler. Based on identified unique/ novel gene, selection of good feed efficient birds can be done that will result in to economic production of broilers in shorter duration and profitable meat production. Also emergent microbial strains will identified by metagenome analysis and their association with good FCR birds.",
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"data-origination": "SUBMITTED"
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"id": "MGYS00001247",
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"bioproject": "PRJEB15485",
"samples-count": 4,
"accession": "MGYS00001247",
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"last-update": "2016-10-04T08:21:22",
"secondary-accession": "ERP017246",
"centre-name": "UNIVERSITY OF HOHENHEIM",
"public-release-date": null,
"study-abstract": "To study the effect on the microbiota of laying hens, dietary treatments were established supplementing a basal diet with prebiotic whey at 6% and probiotic Pediococcus acidilactici. Metagenomic sequences were obtained after DNA isolation from caecal samples",
"study-name": "Metagenomics of laying hens",
"data-origination": "SUBMITTED"
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{
"type": "studies",
"id": "MGYS00001234",
"attributes": {
"bioproject": "PRJEB11550",
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"accession": "MGYS00001234",
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"last-update": "2016-09-28T09:44:18",
"secondary-accession": "ERP012949",
"centre-name": "MHH",
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"study-abstract": "The human diarrheal pathogens Campylobacter jejuni and Campylobacter coli interfere with host innate immune signalling by different means, and their flagellins, FlaA and FlaB, have a low intrinsic property to activate the innate immune receptor TLR5. We have investigated here the hypothesis that the unusual secreted, flagellin-like molecule FlaC present in C. jejuni, C. coli and other Campylobacterales might activate cells via TLR5 and interact with TLR5. FlaC shows a striking sequence identity in its D1 domains to TLR5-activating flagellins of other bacteria such as Salmonella, in contrast to non-stimulating Campylobacter flagellins. We overexpressed and purified FlaC, and tested its immunostimulatory properties on cells of human and chicken origin. Treatment of cells with highly purified FlaC resulted in p38 activation. FlaC directly interacted with TLR5. Preincubation with FlaC decreased the responsiveness of chicken and human macrophages towards the bacterial TLR4 agonist LPS, suggesting that FlaC mediates crosstolerance. C. jejuni flaC mutants induced an increase of cell responses in comparison to the wild type, which was suppressed by genetic complementation. Supplementing excess purified FlaC likewise reduced the cellular response to C. jejuni. In vivo, the administration of ultapure FlaC led to a decrease in caecal IL-1beta expression and a significant change of the caecal microbiota in chickens. We propose that Campylobacter spp. have evolved a novel type of immunostimulatory flagellin-like secreted effector in order to specifically modulate host responses, for example towards other PRR ligands such as LPS.",
"study-name": "Novel immunomodulatory flagellin-like protein FlaC in Campylobacter jejuni and other Campylobacterales",
"data-origination": "SUBMITTED"
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