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"study-abstract": "In many organisms, host-associated microbial communities are acquired horizontally after birth. This process is believed to be shaped by a combination of environmental and host genetic factors. We examined whether genetic variation in animal behavior could affect the composition of the animals microbiota in different environments. The freshwater crustacean Daphnia magna is primarily planktonic, but exhibits variation in the degree to which it browses in benthic sediments. We performed an experiment with clonal lines of D. magna showing different levels of sediment-browsing intensity exposed to either bacteria-rich or bacteria-poor sediment or whose access to sediments was prevented. We find that the bacterial composition of the environment and genotype-specific browsing intensity together influence the composition of the Daphnia-associated bacterial community. Exposure to more diverse bacteria did not lead to a more diverse microbiome, but greater abundances of environment-specific bacteria were found associated with host genotypes that exhibited greater browsing behavior. Our results indicate that, although there is a great deal of variation between individuals, behavior can mediate genotype-by-environment interaction effects on microbiome composition.",
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"study-abstract": "The aim of this study was to investigate the qualitative and quantitative impact that infections by a widespread parasite of cats (i.e. Toxocara cati) exerts on the gut microbiota of feline hosts.",
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"study-abstract": "The aim was to discover if the complex relationship between the host and Giardia are reflected in the faecal bacterial microbiome. Our hypothesis was that Giardia positive dogs and cats have a different microbiome structure and composition to Giardia uninfected animals. For this purpose, we used naturally infected cohorts of dogs and cats infected not only with Giardia, but also with hookworms and coccidia.",
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"study-abstract": "Knight_skin_biogeography - Comparison of skin samples from a rat (mammal), cyclostomid (fish), iguana (reptile), bull frog (amphibian) and a bird (pigeon) to determine if the site chosen to sample on different animals are dependent on site selection.",
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"secondary-accession": "ERP112000",
"centre-name": "QUEEN'S UNIVERSITY BELFAST",
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"study-abstract": "The indiscriminate use of antibiotics in animal production and human consumption is related to the increase of microorganisms resistant to a wide class of chemical compounds. Thus, alternatives are sought for the use of growth promoters and antimicrobials in animal production. Recent research demonstrates the potential of applying essential oils (OEs) in several areas as potential substitutes for antibiotics. This is because they have characteristics similar to these products. However, there are few data in the literature regarding the actions of OEs in axenic cultures of anaerobic ruminal microorganisms. Thus, a project is proposed to: evaluate the efficacy of essential oils from the sequencing of rumen microorganisms of finished cattle in confinement; determine the genes expressed by the ruminal microbiota; identify pure cultures affected by the presence of OEs; to observe the effect of OEs on ruminal bacteria by electron microscopy; to evaluate the microbial resistance of OEs in ruminal bacteria; and evaluate the metatranscriptome of axenic culture of ruminal bacteria cultured with OEs. It is expected to identify species strongly affected by OEs and metabolic routes and mechanisms used by ruminal microorganisms to deal with the presence of OEs and their active compounds. Queen's University of Belfast is part of the Russel Group, which contains the 24 best institutions in the UK. An important part of Queen's University's research is related to food safety. Thus, the university has highly qualified equipment and technical staff for research related to the entire food production chain.",
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"study-abstract": "This study aims to investigate the effect of monensin (Rumensin, Elanco-Eli Lilly Co.) on the microbial community structure of the cow hindgut. Monensin is an ionophore antibiotic administered to cattle and dairy cows to increase their feed efficiency by altering rumen fermentation. Monensin acts by changing the activity of specific metabolic pathways, leading to an increase in propionate concentrations and a decrease in acetate and butyrate concentrations in the cow rumen. Previous studies conducted on the effect of monensin on rumen microbial community structure have led to differing conclusions. In addition, few studies have been conducted to assess the effect of monensin on the microbial community structure elsewhere in the cow digestive tract, such as in the cow hindgut. For the current study, manure was collected, over a period of three months, from eight dairy cows housed at the Teaching and Research Center at Cornell University. Four of the cows were fed a control diet containing no monensin. The other four cows were fed a diet with measured incrementally increasing amounts of monensin. To investigate the effect of monensin on the microbial community composition of the cow hindgut, a total of 184 rectal grab samples were collected from the eight cows over the three month period. Once collected, the samples were processed and stored in a -80degreeC freezer for later microbial community composition analysis. The samples were then extracted using the MO BIO Powersoil-htp 96 Well Soil DNA Isolation Kit and frozen at -80degreeC until they could be sent for further processing and sequencing.",
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"secondary-accession": "ERP017242",
"centre-name": "Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine",
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"study-abstract": "It is unclear how to ensure that the gut microbiota of individuals with disparate dietary practices (DPs) respond consistently to prescribed dietary interventions. To address this, we identified DP-associated gut bacterial taxa in individuals either practicing chronic calorie restriction with adequate nutrition (CRON) or without dietary restrictions (AMER). Transplanted into gnotobiotic mice, AMER and CRON microbiota responded predictably to CRON and AMER diets but with variable response strength. Individual microbiota exist within a population of host communities (metacommunity) connected by microbial exchange. Sequentially cohousing AMER-colonized mice with two different groups of CRON-colonized mice emulated metacommunity effects, resulting in enhanced responses to a CRON diet intervention and changes in several metabolic features in AMER animals. This response was driven by an influx of CRON DP-associated taxa. Certain DPs may impair responses to dietary interventions, necessitating introduction of absent diet-responsive bacterial lineages present in other individuals and identified using the strategies described.",
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"last-update": "2018-11-21T10:54:10",
"secondary-accession": "ERP024389",
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"study-abstract": "Antimicrobial resistance (AMR) in bacteria and associated morbidity and mortality is increasing. Use of antimicrobials for livestock selects for AMR that can subsequently be transferred to the human reservoir. This flow of AMR between reservoirs demands surveillance in livestock as well as in humans. As part of the EFFORT project (http://www.effort-against-amr.eu/), we have quantified and characterized the acquired resistance gene pools (resistomes) of 181 pig and 178 poultry farms from nine European countries, generating more than 5,000 Gigabases of DNA sequence, using shotgun metagenomics. The pig and poultry resistomes were very different in abundance and composition. There was a significant country effect on the resistomes, more so in pigs than poultry. We found higher AMR loads in pigs, while poultry resistomes were more diverse. We detected several newly described, critical AMR genes, including mcr-1 and optrA, which differed both between host species and countries. We found that the total AMR level, was associated with the overall country-specific antimicrobial usage in livestock and that countries with comparable usage patterns have similar resistomes.",
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"study-abstract": "Parasitic gastrointestinal nematodes contribute to significant human morbidity and cause billions of dollars per year in lost agricultural production. Control is dependent on the use of anthelmintic drugs, which in the case of livestock parasites, are severely compromised by the widespread development of drug resistance. More recently, there are concerns regarding the emergence of anthelmintic resistance in human parasitic nematodes in response to the selection pressure resulting from mass drug administration (MDA) programs. Consequently, there is an urgent need for sensitive, scalable and accurate diagnostic tools to detect the emergence of anthelmintic resistance.. Detecting and measuring the frequency of resistance-associated mutations in parasite populations has the potential to provide sensitive and quantitative assessment of resistance emergence from an early stage. We describe the development and validation of deep-amplicon sequencing as a powerful new approach to detect and quantify the frequency of single nucleotide polymorphisms (SNPs) associated with benzimidazole resistance. We have used parasite communities in sheep, to undertake a proof-of-concept study of this approach. Sheep provide an excellent host system, as there are multiple co-infecting trichostrongylid nematode species, each with varying prevalence of benzimidazole resistance. We demonstrate that the approach provides an accurate measure of resistance allele frequencies, and can reliably detect resistance alleles down to a frequency of 0.1%, making it particularly valuable for screening mutations in the early stages of resistance. We illustrate the power of the technique by screening UK sheep flocks for benzimidazole resistance-associated SNPs at three different codons of the β-tubulin gene, in seven different parasite species from 164 populations (95 from ewes and 69 from lambs) in a single MiSeq sequencing run. This approach provides a powerful new tool to screen for the emergence of anthelmintic resistance mutations in parasitic nematode populations of both animals and humans.",
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