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"study-abstract": "Human-associated archaea remain understudied in the field of microbiome research, although in particular methanogenic archaea have been found to be regular commensals of the human gut, and represent keystone species in metabolic processes.Knowledge on the abundance and diversity of human-associated archaea is extremely limited, and little is known about their function(s), their overall role in human health, or their association with other parts of the human body, besides the gastro-intestinal tract and oral cavity. Currently, methodological issues impede the full assessment of the human archaeome, as bacteria-targeting protocols are unsuitable to characterize the full spectrum of Archaea.The goal of this study was to critically assess PCR-based methods for specific Archaea detection in human tissue samples. We tested approaches to specifically detect M. smithii, M. stadtmanae and M. luminyensis, and to assess the overall archaeal abundance and diversity using next generation sequencing based technology. To test our established protocols, we determined the archaeal diversity associated with human skin, lung (bronchoalveolar lavage), gastrointestinal tract, stool and nose.Detection of Archaea was highly dependent on primer selection and sequence processing pipeline. Our proposed protocol enabled us to retrieve a novel picture of the human archaeome, as we identified for the first time Methanobacterium and Woesearchaeota (DPANN superphylum) to be associated with the human gastrointestinal tract and the human lung, respectively. Similar to bacteria, human-associated archaeal communities were found to group biogeographically, forming (i) the thaumarchaeal skin landscape, (ii) the (methano)euryarchaeal GIT, (iii) a mixed skin/GIT landscape for the nose, and (iv) a woesearchaeal lung landscape.Our study highlights the importance of primer and bioinformatics pipeline choice for studying the human archaeome. We were able to establish protocols that enlightened the presence of yet undetected Archaea in all investigated tissue samples and to detect biogeographic patterns of the human archaeome in respiratory tract, the gastrointestinal tract and on skin. Our results are a solid basis for further investigation of the human archaeome, and in the long term to uncover the potential archaeal role in human health and disease.",
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"study-abstract": "Microbiota as a functional assemblage of microbes plays an important role in environment and in lives of multicellular organisms. Animal gut microbiota is strongly influenced by dietary factors while soil microbial flora can be shaped by various physical, chemical, and biological conditions.",
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"study-abstract": "OVERALL STUDY AIM\nWe do not fully understand how important types (species) of bacteria and packages of genetic material (genes) coding for antibiotic resistance move between humans, animals and the environment, or where, how and why antibiotic resistance emerges. This study aims to look in detail at the genetic level at bacteria in farm animals, human/animal sewage, sewage treatment works and rivers, to work out the complex network of transmission of important antibiotic-resistant bacteria and antibiotic resistance genes. We will use this information to work out how best to slow down the spread of antibiotic resistance between humans, livestock and the environment.\n\nSTUDY BACKGROUND AND AIMS IN MORE DETAIL\nInfections are one of the most common causes of ill-health in human and animal medicine, and are caused by a range of different micro-organisms, including viruses and bacteria. Amongst bacteria, there are some species, or types, of bacteria, which can live harmlessly in human and animal intestines, sewage, and rivers, but can also cause disease in humans and animals if they get into the wrong body space, such as the bloodstream or urine. Examples of these bacteria include E. coli, and other similar organisms, which belong to a family of bacteria called \"Enterobacteriaceae\".It has generally been possible to treat infections caused by bacteria using several classes of medicines, known as antibiotics. Different antibiotics kill bacteria in different ways: for example, they can switch off critical chemical processes that the bacteria need to survive, or they can break down the outer shell of the bacteria. In response to the use of antibiotics, bacteria have changed over time, finding ways to alter their structure so that antibiotics no longer have a target to act on, or by producing substances that break down the antibiotic before it has a chance to kill the bacteria. These changes to the bacteria's genetic code, so that they are no longer killed by an antibiotic, create antibiotic resistance. Bacteria can also acquire packages of genes that cause antibiotic resistance from other surrounding bacteria. This is known as horizontal gene transfer. Through these mechanisms, members of the Enterobacteriaceae family of bacteria have developed antibiotic resistance to a number of different antibiotics over a short period of time. In some cases we are no longer able to treat these infections with the antibiotics we have available.Studying antibiotic resistance and horizontal gene transfer in bacteria found in humans, animals and the environment is difficult because we cannot directly see how bacteria and their genetic material move between them. However, new \"Next Generation Sequencing\" (NGS) technologies allow scientists to look in great detail at the genetic code of large numbers of bacteria. Comparing this information across bacteria which have been living in the different parts of the environment (e.g. sewage treatment works, rivers) and in human and animal sewage allows us to see how bacteria have evolved to become resistant to antibiotics, and how resistance genes have been shared between them.This study will use NGS technologies to look at the genetic code of large numbers of Enterobacteriaceae bacteria found in humans, animals (pigs, sheep and poultry), sewage (pre-, during and post-treatment), and rivers. These different groups/areas will be sampled in different seasons of one calendar year to determine how antibiotic resistance genes move around between these locations and over time, and what factors might influence this movement. We will also be investigating whether various chemicals and nutrients in the water may be affecting how quickly horizontal gene transfer occurs. Understanding this is essential to work out how we might intervene more effectively to slow the spread of antibiotic resistance genes and bacteria, and keep our antibiotic medicines useful.",
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"id": "MGYS00005524",
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"last-update": "2020-06-14T14:49:38",
"secondary-accession": "ERP108642",
"centre-name": "IFIK",
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"study-abstract": "Background: Prior studies have demonstrated an influence of the environment on the human nasal microbiota, particularly in the case of pig farming. However, very little is known about the impact of season on the dynamics of the microbiota in a pig farm setting. Methods: We performed a longitudinal study, investigating the changes in the nasal microbiota of different samples collected in the four seasons (winter, spring, summer and fall). We collected samples from 30 pig farms in Switzerland in each season from 2014-2015. This included nasal swabs from pigs (n=225), air samples taken in the pig confinement building (n=105), and nasal swabs from pig farmers working in these pig farms (n=154 from 48 pig farmers). As controls, nasal swabs from cow farmers (n=56 from 18 cow farmers) and individuals with no contact with farm animals (n=69 from 24 non-exposed individuals) were collected. Analysis of the microbiota was performed based on 16S rRNA high-throughput sequencing utilizing the Illumina MiSeq platform and the recently developed DADA2 pipeline. Results: Alpha-diversity values were generally higher in samples received in winter with the exception of samples from the non-exposed controls which displayed low alpha-diversity values throughout the seasons with no significant differences. The microbial structure of pig farmers, cow farmers and non-exposed individuals was significantly influenced by season. Also, the farm where the samples were taken from influenced the nasal microbiota of pig and cow farmers. There was a stronger similarity for samples that originated from the same farm as compared to samples from different farms in winter and this farm-specificity was partially or completely lost in spring, summer and fall.Conclusions: Nasal microbiota of pig farmers is affected by the regular exposure to pigs throughout the year. However, season has a very strong effect on the nasal microbiota of pig farmers, pigs, and cow farmers, as well as the airborne bacterial composition. This seasonal effect is much weaker in individuals without any contact with farm animals.",
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{
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"last-update": "2020-06-14T14:34:33",
"secondary-accession": "ERP109599",
"centre-name": "NIOO KNAW",
"public-release-date": null,
"study-abstract": "We studied the legacy effects of plants on fungal and bacterial communities in soils, roots, leaves and caterpillars.",
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{
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"last-update": "2020-06-14T13:40:21",
"secondary-accession": "SRP094801",
"centre-name": "City University of Hong Kong",
"public-release-date": null,
"study-abstract": "16S rRNA sequencing reads from samples of household surfaces, residents'' skin and household air in Hong Kong residences.",
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"last-update": "2020-06-14T13:39:06",
"secondary-accession": "ERP017451",
"centre-name": "AALBORG UNIVERSITY",
"public-release-date": null,
"study-abstract": "High throughput characterisation of microbial communities is widely used as a source of information to develop strategies for improved biological processes in humans, animals and engineered systems. However, the introduction of organisms that do not contribute or grow in the system can ruin conclusions derived from the composition. In this study we sequenced samples from digesters and their influent streams to evaluate which organisms were truly growing and which were probably just continuously fed into the system.",
"study-name": "Microbial analysis is challenged by immigration",
"data-origination": "SUBMITTED"
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{
"type": "studies",
"id": "MGYS00005507",
"attributes": {
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"samples-count": 1055,
"accession": "MGYS00005507",
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"last-update": "2020-06-06T21:56:59",
"secondary-accession": "ERP005870",
"centre-name": "IMPERIAL COLLEGE",
"public-release-date": null,
"study-abstract": "The NeoM (Neonatal Microbiota) Study is an ecological study investigating the microbiota of pre-term infants. Samples collected include faecal samples, skin swabs and swabs of infant incubators. Bacterial DNA was extracted from the samples using either MPBio FastDNA Spin kits or MPBio FastDNA Spin Kits for Soil and V3-V5 amplicons were generated using Bifidobacterium-optomised primers (Sim et al, 2012, PLOS ONE) and tagged with 12bp barcodes. These were then sequenced using a 454 Life Sciences GS FLX (Roche) following the Roche Amplicon Lib-L protocol. Both raw data (.sff files) and data denoised via ampliconnoise.py (as part of the Qiime pipeline) will be submitted here.",
"study-name": "A collection of 16S reads for samples relating to pre-term infants",
"data-origination": "SUBMITTED"
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"last-update": "2020-05-31T09:53:57",
"secondary-accession": "ERP010047",
"centre-name": "UTK",
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"study-abstract": "Try to identify the microorganisms responsible for dechlorination and their functional genes.",
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"data-origination": "SUBMITTED"
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