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Earth microbiome project

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https://www.readbyqxmd.com/read/27822515/open-source-sequence-clustering-methods-improve-the-state-of-the-art
#1
Evguenia Kopylova, Jose A Navas-Molina, Céline Mercier, Zhenjiang Zech Xu, Frédéric Mahé, Yan He, Hong-Wei Zhou, Torbjørn Rognes, J Gregory Caporaso, Rob Knight
Sequence clustering is a common early step in amplicon-based microbial community analysis, when raw sequencing reads are clustered into operational taxonomic units (OTUs) to reduce the run time of subsequent analysis steps. Here, we evaluated the performance of recently released state-of-the-art open-source clustering software products, namely, OTUCLUST, Swarm, SUMACLUST, and SortMeRNA, against current principal options (UCLUST and USEARCH) in QIIME, hierarchical clustering methods in mothur, and USEARCH's most recent clustering algorithm, UPARSE...
January 2016: MSystems
https://www.readbyqxmd.com/read/27602409/extreme-dysbiosis-of-the-microbiome-in-critical-illness
#2
Daniel McDonald, Gail Ackermann, Ludmila Khailova, Christine Baird, Daren Heyland, Rosemary Kozar, Margot Lemieux, Karrie Derenski, Judy King, Christine Vis-Kampen, Rob Knight, Paul E Wischmeyer
Critical illness is hypothesized to associate with loss of "health-promoting" commensal microbes and overgrowth of pathogenic bacteria (dysbiosis). This dysbiosis is believed to increase susceptibility to nosocomial infections, sepsis, and organ failure. A trial with prospective monitoring of the intensive care unit (ICU) patient microbiome using culture-independent techniques to confirm and characterize this dysbiosis is thus urgently needed. Characterizing ICU patient microbiome changes may provide first steps toward the development of diagnostic and therapeutic interventions using microbiome signatures...
July 2016: MSphere
https://www.readbyqxmd.com/read/27114874/characterization-of-microbial-associations-with-methanotrophic-archaea-and-sulfate-reducing-bacteria-through-statistical-comparison-of-nested-magneto-fish-enrichments
#3
Elizabeth Trembath-Reichert, David H Case, Victoria J Orphan
Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range of Deltaproteobacteria diversity...
2016: PeerJ
https://www.readbyqxmd.com/read/27025932/the-first-space-related-study-of-a-kombucha-multimicrobial-cellulose-forming-community-preparatory-laboratory-experiments
#4
O Podolich, I Zaets, O Kukharenko, I Orlovska, O Reva, L Khirunenko, M Sosnin, A Haidak, S Shpylova, I Rohutskyy, A Kharina, М Skoryk, M Kremenskoy, D Klymchuk, R Demets, J-P de Vera, N Kozyrovska
Biofilm-forming microbial communities are known as the most robust assemblages that can survive in harsh environments. Biofilm-associated microorganisms display greatly increased resistance to physical and chemical adverse conditions, and they are expected to be the first form of life on Earth or anywhere else. Biological molecules synthesized by biofilm -protected microbiomes may serve as markers of the nucleoprotein life. We offer a new experimental model, a kombucha multimicrobial culture (KMC), to assess a structural integrity of a widespread microbial polymer - cellulose - as a biosignature of bacteria-producers for the multipurpose international project "BIOlogical and Mars Experiment (BIOMEX)", which aims to study the vitality of pro- and eukaryotic organisms and the stability of organic biomolecules in contact with minerals to analyze the detectability of life markers in the context of a planetary background...
March 30, 2016: Origins of Life and Evolution of the Biosphere
https://www.readbyqxmd.com/read/26914164/spatial-scale-drives-patterns-in-soil-bacterial-diversity
#5
Sarah L O'Brien, Sean M Gibbons, Sarah M Owens, Jarrad Hampton-Marcell, Eric R Johnston, Julie D Jastrow, Jack A Gilbert, Folker Meyer, Dionysios A Antonopoulos
Soil microbial communities are essential for ecosystem function, but linking community composition to biogeochemical processes is challenging because of high microbial diversity and large spatial variability of most soil characteristics. We investigated soil bacterial community structure in a switchgrass stand planted on soil with a history of grassland vegetation at high spatial resolution to determine whether biogeographic trends occurred at the centimeter scale. Moreover, we tested whether such heterogeneity, if present, influenced community structure within or among ecosystems...
June 2016: Environmental Microbiology
https://www.readbyqxmd.com/read/26645377/personalized-medicine-beyond-genomics-alternative-futures-in-big-data-proteomics-environtome-and-the-social-proteome
#6
Vural Özdemir, Edward S Dove, Ulvi K Gürsoy, Semra Şardaş, Arif Yıldırım, Şenay Görücü Yılmaz, I Ömer Barlas, Kıvanç Güngör, Alper Mete, Sanjeeva Srivastava
No field in science and medicine today remains untouched by Big Data, and psychiatry is no exception. Proteomics is a Big Data technology and a next generation biomarker, supporting novel system diagnostics and therapeutics in psychiatry. Proteomics technology is, in fact, much older than genomics and dates to the 1970s, well before the launch of the international Human Genome Project. While the genome has long been framed as the master or "elite" executive molecule in cell biology, the proteome by contrast is humble...
December 8, 2015: Journal of Neural Transmission
https://www.readbyqxmd.com/read/26568626/metabolic-network-guided-binning-of-metagenomic-sequence-fragments
#7
Matthew B Biggs, Jason A Papin
MOTIVATION: Most microbes on Earth have never been grown in a laboratory, and can only be studied through DNA sequences. Environmental DNA sequence samples are complex mixtures of fragments from many different species, often unknown. There is a pressing need for methods that can reliably reconstruct genomes from complex metagenomic samples in order to address questions in ecology, bioremediation, and human health. RESULTS: We present the SOrting by NEtwork Completion (SONEC) approach for assigning reactions to incomplete metabolic networks based on a metabolite connectivity score...
March 15, 2016: Bioinformatics
https://www.readbyqxmd.com/read/25970595/patterns-of-gut-bacterial-colonization-in-three-primate-species
#8
Erin A McKenney, Allen Rodrigo, Anne D Yoder
Host fitness is impacted by trillions of bacteria in the gastrointestinal tract that facilitate development and are inextricably tied to life history. During development, microbial colonization primes the gut metabolism and physiology, thereby setting the stage for adult nutrition and health. However, the ecological rules governing microbial succession are poorly understood. In this study, we examined the relationship between host lineage, captive diet, and life stage and gut microbiota characteristics in three primate species (infraorder, Lemuriformes)...
2015: PloS One
https://www.readbyqxmd.com/read/25368606/phylogenetic-signal-in-the-community-structure-of-host-specific-microbiomes-of-tropical-marine-sponges
#9
Cole G Easson, Robert W Thacker
Sponges (Porifera) can host diverse and abundant communities of microbial symbionts that make crucial contributions to host metabolism. Although these communities are often host-specific and hypothesized to co-evolve with their hosts, correlations between host phylogeny and microbiome community structure are rarely tested. As part of the Earth Microbiome Project (EMP), we surveyed the microbiomes associated with 20 species of tropical marine sponges collected over a narrow geographic range. We tested whether (1) univariate metrics of microbiome diversity displayed significant phylogenetic signal across the host phylogeny; (2) host identity and host phylogeny were significant factors in multivariate analyses of taxonomic and phylogenetic dissimilarity; and (3) different minimum read thresholds impacted these results...
2014: Frontiers in Microbiology
https://www.readbyqxmd.com/read/25184604/the-earth-microbiome-project-successes-and-aspirations
#10
Jack A Gilbert, Janet K Jansson, Rob Knight
No abstract text is available yet for this article.
2014: BMC Biology
https://www.readbyqxmd.com/read/25177538/subsampled-open-reference-clustering-creates-consistent-comprehensive-otu-definitions-and-scales-to-billions-of-sequences
#11
Jai Ram Rideout, Yan He, Jose A Navas-Molina, William A Walters, Luke K Ursell, Sean M Gibbons, John Chase, Daniel McDonald, Antonio Gonzalez, Adam Robbins-Pianka, Jose C Clemente, Jack A Gilbert, Susan M Huse, Hong-Wei Zhou, Rob Knight, J Gregory Caporaso
We present a performance-optimized algorithm, subsampled open-reference OTU picking, for assigning marker gene (e.g., 16S rRNA) sequences generated on next-generation sequencing platforms to operational taxonomic units (OTUs) for microbial community analysis. This algorithm provides benefits over de novo OTU picking (clustering can be performed largely in parallel, reducing runtime) and closed-reference OTU picking (all reads are clustered, not only those that match a reference database sequence with high similarity)...
2014: PeerJ
https://www.readbyqxmd.com/read/24841417/human-and-environmental-impacts-on-river-sediment-microbial-communities
#12
Sean M Gibbons, Edwin Jones, Angelita Bearquiver, Frederick Blackwolf, Wayne Roundstone, Nicole Scott, Jeff Hooker, Robert Madsen, Maureen L Coleman, Jack A Gilbert
Sediment microbial communities are responsible for a majority of the metabolic activity in river and stream ecosystems. Understanding the dynamics in community structure and function across freshwater environments will help us to predict how these ecosystems will change in response to human land-use practices. Here we present a spatiotemporal study of sediments in the Tongue River (Montana, USA), comprising six sites along 134 km of river sampled in both spring and fall for two years. Sequencing of 16S rRNA amplicons and shotgun metagenomes revealed that these sediments are the richest (∼ 65,000 microbial 'species' identified) and most novel (93% of OTUs do not match known microbial diversity) ecosystems analyzed by the Earth Microbiome Project to date, and display more functional diversity than was detected in a recent review of global soil metagenomes...
2014: PloS One
https://www.readbyqxmd.com/read/24774752/protocols-for-metagenomic-dna-extraction-and-illumina-amplicon-library-preparation-for-faecal-and-swab-samples
#13
A-T E Vo, J A Jedlicka
Next-generation sequencing (NGS) technology has extraordinarily enhanced the scope of research in the life sciences. To broaden the application of NGS to systems that were previously difficult to study, we present protocols for processing faecal and swab samples into amplicon libraries amenable to Illumina sequencing. We developed and tested a novel metagenomic DNA extraction approach using solid phase reversible immobilization (SPRI) beads on Western Bluebird (Sialia mexicana) samples stored in RNAlater. Compared with the MO BIO PowerSoil Kit, the current standard for the Human and Earth Microbiome Projects, the SPRI-based method produced comparable 16S rRNA gene PCR amplification from faecal extractions but significantly greater DNA quality, quantity and PCR success for both cloacal and oral swab samples...
November 2014: Molecular Ecology Resources
https://www.readbyqxmd.com/read/24280061/emperor-a-tool-for-visualizing-high-throughput-microbial-community-data
#14
Yoshiki Vázquez-Baeza, Meg Pirrung, Antonio Gonzalez, Rob Knight
BACKGROUND: As microbial ecologists take advantage of high-throughput sequencing technologies to describe microbial communities across ever-increasing numbers of samples, new analysis tools are required to relate the distribution of microbes among larger numbers of communities, and to use increasingly rich and standards-compliant metadata to understand the biological factors driving these relationships. In particular, the Earth Microbiome Project drives these needs by profiling the genomic content of tens of thousands of samples across multiple environment types...
2013: GigaScience
https://www.readbyqxmd.com/read/23587224/the-biological-observation-matrix-biom-format-or-how-i-learned-to-stop-worrying-and-love-the-ome-ome
#15
Daniel McDonald, Jose C Clemente, Justin Kuczynski, Jai Ram Rideout, Jesse Stombaugh, Doug Wendel, Andreas Wilke, Susan Huse, John Hufnagle, Folker Meyer, Rob Knight, J Gregory Caporaso
BACKGROUND: We present the Biological Observation Matrix (BIOM, pronounced "biome") format: a JSON-based file format for representing arbitrary observation by sample contingency tables with associated sample and observation metadata. As the number of categories of comparative omics data types (collectively, the "ome-ome") grows rapidly, a general format to represent and archive this data will facilitate the interoperability of existing bioinformatics tools and future meta-analyses. FINDINGS: The BIOM file format is supported by an independent open-source software project (the biom-format project), which initially contains Python objects that support the use and manipulation of BIOM data in Python programs, and is intended to be an open development effort where developers can submit implementations of these objects in other programming languages...
2012: GigaScience
https://www.readbyqxmd.com/read/22134646/an-improved-greengenes-taxonomy-with-explicit-ranks-for-ecological-and-evolutionary-analyses-of-bacteria-and-archaea
#16
Daniel McDonald, Morgan N Price, Julia Goodrich, Eric P Nawrocki, Todd Z DeSantis, Alexander Probst, Gary L Andersen, Rob Knight, Philip Hugenholtz
Reference phylogenies are crucial for providing a taxonomic framework for interpretation of marker gene and metagenomic surveys, which continue to reveal novel species at a remarkable rate. Greengenes is a dedicated full-length 16S rRNA gene database that provides users with a curated taxonomy based on de novo tree inference. We developed a 'taxonomy to tree' approach for transferring group names from an existing taxonomy to a tree topology, and used it to apply the Greengenes, National Center for Biotechnology Information (NCBI) and cyanoDB (Cyanobacteria only) taxonomies to a de novo tree comprising 408,315 sequences...
March 2012: ISME Journal
https://www.readbyqxmd.com/read/21304728/the-earth-microbiome-project-meeting-report-of-the-1-emp-meeting-on-sample-selection-and-acquisition-at-argonne-national-laboratory-october-6-2010
#17
Jack A Gilbert, Folker Meyer, Janet Jansson, Jeff Gordon, Norman Pace, James Tiedje, Ruth Ley, Noah Fierer, Dawn Field, Nikos Kyrpides, Frank-Oliver Glöckner, Hans-Peter Klenk, K Eric Wommack, Elizabeth Glass, Kathryn Docherty, Rachel Gallery, Rick Stevens, Rob Knight
This report details the outcome the first meeting of the Earth Microbiome Project to discuss sample selection and acquisition. The meeting, held at the Argonne National Laboratory on Wednesday October 6(th) 2010, focused on discussion of how to prioritize environmental samples for sequencing and metagenomic analysis as part of the global effort of the EMP to systematically determine the functional and phylogenetic diversity of microbial communities across the world.
2010: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/21304727/meeting-report-the-terabase-metagenomics-workshop-and-the-vision-of-an-earth-microbiome-project
#18
Jack A Gilbert, Folker Meyer, Dion Antonopoulos, Pavan Balaji, C Titus Brown, Christopher T Brown, Narayan Desai, Jonathan A Eisen, Dirk Evers, Dawn Field, Wu Feng, Daniel Huson, Janet Jansson, Rob Knight, James Knight, Eugene Kolker, Kostas Konstantindis, Joel Kostka, Nikos Kyrpides, Rachel Mackelprang, Alice McHardy, Christopher Quince, Jeroen Raes, Alexander Sczyrba, Ashley Shade, Rick Stevens
Between July 18(th) and 24(th) 2010, 26 leading microbial ecology, computation, bioinformatics and statistics researchers came together in Snowbird, Utah (USA) to discuss the challenge of how to best characterize the microbial world using next-generation sequencing technologies. The meeting was entitled "Terabase Metagenomics" and was sponsored by the Institute for Computing in Science (ICiS) summer 2010 workshop program. The aim of the workshop was to explore the fundamental questions relating to microbial ecology that could be addressed using advances in sequencing potential...
2010: Standards in Genomic Sciences
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