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Microbiome bioinformatics

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https://www.readbyqxmd.com/read/28625995/novel-antibiotic-resistance-determinants-from-agricultural-soil-exposed-to-antibiotics-widely-used-in-human-medicine-and-animal-farming
#1
Calvin Ho-Fung Lau, Kalene van Engelen, Stephen Gordon, Justin Renaud, Edward Topp
Antibiotic resistance has emerged globally as one of the biggest threats to human and animal health. Although the excessive use of antibiotics is recognized for accelerating the selection for resistance, there is a growing body of evidence suggesting that natural environments are "hotspots" for the development of both ancient and contemporary resistance mechanisms. Given that pharmaceuticals can be entrained onto agricultural land through anthropogenic activities, this could be a potential driver for the emergence and dissemination of resistance in soil bacteria...
June 16, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28621304/epigenetic-and-gene-expression-analysis-of-ankylosing-spondylitis-associated-loci-implicate-immune-cells-and-the-gut-in-the-disease-pathogenesis
#2
Z Li, K Haynes, D J Pennisi, L K Anderson, X Song, G P Thomas, T Kenna, P Leo, M A Brown
Ankylosing spondylitis (AS) is a common immune-mediated arthropathy primarily affecting the spine and pelvis. Most AS patients have subclinical intestinal inflammation, suggesting the gut microbiome and the immune response play a role in pathogenesis. Susceptibility to AS is primarily genetic, and at least 114 susceptibility variants have been identified to date. We applied bioinformatic methods utilizing epigenetic and gene and protein expression data to identify the cell types through which AS-associated variants operate...
June 15, 2017: Genes and Immunity
https://www.readbyqxmd.com/read/28609785/comprehensive-analysis-of-microorganisms-accompanying-human-archaeological-remains
#3
Anna Philips, Ireneusz Stolarek, Bogna Kuczkowska, Anna Juras, Luiza Handschuh, Janusz Piontek, Piotr Kozlowski, Marek Figlerowicz
Background.: Metagenome analysis has become a common source of information about microbial communities that occupy a wide range of niches, including archaeological specimens. It has been shown that vast majority of DNA extracted from ancient samples come from bacteria (presumably modern contaminants). However, characterization of microbial DNA accompanying human remains has never been done systematically for a wide range of different samples. Findings.: We used metagenomic approaches to perform comparative analyses of microorganism communities present in 161 archaeological human remains...
June 13, 2017: GigaScience
https://www.readbyqxmd.com/read/28609295/clubber-removing-the-bioinformatics-bottleneck-in-big-data-analyses
#4
Maximilian Miller, Chengsheng Zhu, Yana Bromberg
With the advent of modern day high-throughput technologies, the bottleneck in biological discovery has shifted from the cost of doing experiments to that of analyzing results. clubber is our automated cluster-load balancing system developed for optimizing these "big data" analyses. Its plug-and-play framework encourages re-use of existing solutions for bioinformatics problems. clubber's goals are to reduce computation times and to facilitate use of cluster computing. The first goal is achieved by automating the balance of parallel submissions across available high performance computing (HPC) resources...
June 13, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28560604/anthropogenic-protection-alters-the-microbiome-in-intertidal-mangrove-wetlands-in-hainan-island
#5
Juanli Yun, Yongcui Deng, Hongxun Zhang
Intertidal mangrove wetlands are of great economic and ecological importance. The regular influence of tides has led to the microbial communities in these wetlands differing significantly from those in other habitats. In this study, we investigated the microbiomes of the two largest mangrove wetlands in Hainan Island, China, which have different levels of anthropogenic protection. Soil samples were collected from the root zone of 13 mangrove species. The microbial composition, including key functional groups, was assessed using Illumina sequencing...
May 30, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28542523/impact-of-maintenance-immunosuppressive-therapy-on-the-fecal-microbiome-of-renal-transplant-recipients-comparison-between-an-everolimus-and-a-standard-tacrolimus-based-regimen
#6
Gianluigi Zaza, Alessandra Dalla Gassa, Giovanna Felis, Simona Granata, Sandra Torriani, Antonio Lupo
BACKGROUND: The gut microbiome is the full set of microbes living in the gastrointestinal tract and is emerging as an important dynamic/fluid system that, if altered by environmental, dietetic or pharmacological factors, could considerably influence drug response. However, the immunosuppressive drug-induced modifications of this system are still poorly defined. METHODS: We employed an innovative bioinformatics approach to assess differences in the whole-gut microbial metagenomic profile of 20 renal transplant recipients undergoing maintenance treatment with two different immunosuppressive protocols...
2017: PloS One
https://www.readbyqxmd.com/read/28509357/characterization-of-microbial-mixtures-by-mass-spectrometry
#7
REVIEW
Todd R Sandrin, Plamen A Demirev
MS applications in microbiology have increased significantly in the past 10 years, due in part to the proliferation of regulator-approved commercial MALDI MS platforms for rapid identification of clinical infections. In parallel, with the expansion of MS technologies in the "omics" fields, novel MS-based research efforts to characterize organismal as well as environmental microbiomes have emerged. Successful characterization of microorganisms found in complex mixtures of other organisms remains a major challenge for researchers and clinicians alike...
May 16, 2017: Mass Spectrometry Reviews
https://www.readbyqxmd.com/read/28505251/false-discovery-rate-control-incorporating-phylogenetic-tree-increases-detection-power-in-microbiome-wide-multiple-testing
#8
Jian Xiao, Hongyuan Cao, Jun Chen
Motivation: Next generation sequencing technologies have enabled the study of the human microbiome through direct sequencing of microbial DNA, resulting in an enormous amount of microbiome sequencing data. One unique characteristic of microbiome data is the phylogenetic tree that relates all the bacterial species. Closely related bacterial species have a tendency to exhibit a similar relationship with the environment or disease. Thus, incorporating the phylogenetic tree information can potentially improve the detection power for microbiome-wide association studies, where hundreds or thousands of tests are conducted simultaneously to identify bacterial species associated with a phenotype of interest...
May 13, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28481971/bioinformatics-tools-for-quantitative-and-functional-metagenome-and-metatranscriptome-data-analysis-in-microbes
#9
Sheng-Yong Niu, Jinyu Yang, Adam McDermaid, Jing Zhao, Yu Kang, Qin Ma
Metagenomic and metatranscriptomic sequencing approaches are more frequently being used to link microbiota to important diseases and ecological changes. Many analyses have been used to compare the taxonomic and functional profiles of microbiota across habitats or individuals. While a large portion of metagenomic analyses focus on species-level profiling, some studies use strain-level metagenomic analyses to investigate the relationship between specific strains and certain circumstances. Metatranscriptomic analysis provides another important insight into activities of genes by examining gene expression levels of microbiota...
May 8, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28467461/16s-rrna-gene-sequencing-and-healthy-reference-ranges-for-28-clinically-relevant-microbial-taxa-from-the-human-gut-microbiome
#10
Daniel E Almonacid, Laurens Kraal, Francisco J Ossandon, Yelena V Budovskaya, Juan Pablo Cardenas, Elisabeth M Bik, Audrey D Goddard, Jessica Richman, Zachary S Apte
Changes in the relative abundances of many intestinal microorganisms, both those that naturally occur in the human gut microbiome and those that are considered pathogens, have been associated with a range of diseases. To more accurately diagnose health conditions, medical practitioners could benefit from a molecular, culture-independent assay for the quantification of these microorganisms in the context of a healthy reference range. Here we present the targeted sequencing of the microbial 16S rRNA gene of clinically relevant gut microorganisms as a method to provide a gut screening test that could assist in the clinical diagnosis of certain health conditions...
2017: PloS One
https://www.readbyqxmd.com/read/28439121/bioinformatic-approaches-including-predictive-metagenomic-profiling-reveal-characteristics-of-bacterial-response-to-petroleum-hydrocarbon-contamination-in-diverse-environments
#11
Arghya Mukherjee, Bobby Chettri, James S Langpoklakpam, Pijush Basak, Aravind Prasad, Ashis K Mukherjee, Maitree Bhattacharyya, Arvind K Singh, Dhrubajyoti Chattopadhyay
Microbial remediation of oil polluted habitats remains one of the foremost methods for restoration of petroleum hydrocarbon contaminated environments. The development of effective bioremediation strategies however, require an extensive understanding of the resident microbiome of these habitats. Recent developments such as high-throughput sequencing has greatly facilitated the advancement of microbial ecological studies in oil polluted habitats. However, effective interpretation of biological characteristics from these large datasets remain a considerable challenge...
April 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28431529/hirbin-high-resolution-identification-of-differentially-abundant-functions-in-metagenomes
#12
Tobias Österlund, Viktor Jonsson, Erik Kristiansson
BACKGROUND: Gene-centric analysis of metagenomics data provides information about the biochemical functions present in a microbiome under a certain condition. The ability to identify significant differences in functions between metagenomes is dependent on accurate classification and quantification of the sequence reads (binning). However, biological effects acting on specific functions may be overlooked if the classes are too general. METHODS: Here we introduce High-Resolution Binning (HirBin), a new method for gene-centric analysis of metagenomes...
April 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28398468/rtk-efficient-rarefaction-analysis-of-large-datasets
#13
Paul Saary, Kristoffer Forslund, Peer Bork, Falk Hildebrand
Motivation: The rapidly expanding microbiomics field is generating increasingly larger datasets, characterizing the microbiota in diverse environments. Although classical numerical ecology methods provide a robust statistical framework for their analysis, software currently available is inadequate for large datasets and some computationally intensive tasks, like rarefaction and associated analysis. Results: Here we present a software package for rarefaction analysis of large count matrices, as well as estimation and visualization of diversity, richness and evenness...
April 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28390576/functional-relevance-of-microbiome-signatures-the-correlation-era-requires-tools-for-consolidation
#14
Ludovica F Buttó, Dirk Haller
Compelling research over the past decade identified a fundamental role of the intestinal microbiome on human health. Compositional and functional changes of this microbial ecosystem are correlated with a variety of human pathologies. Metagenomic resolution and bioinformatic tools considerably improved, allowing even strain-level analysis. However, the search for microbial risk patterns in human cohorts is often confounded by environmental factors (eg, medication) and host status (eg, disease relapse), questioning the prognostic and therapeutic value of the currently available information...
April 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28384412/second-era-of-omics-in-caries-research-moving-past-the-phase-of-disillusionment
#15
M M Nascimento, E Zaura, A Mira, N Takahashi, J M Ten Cate
Novel approaches using OMICS techniques enable a collective assessment of multiple related biological units, including genes, gene expression, proteins, and metabolites. In the past decade, next-generation sequencing ( NGS) technologies were improved by longer sequence reads and the development of genome databases and user-friendly pipelines for data analysis, all accessible at lower cost. This has generated an outburst of high-throughput data. The application of OMICS has provided more depth to existing hypotheses as well as new insights in the etiology of dental caries...
April 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28361558/mining-the-fecal-proteome-from-biomarkers-to-personalised-medicine
#16
Ping Jin, Kui Wang, Canhua Huang, Edouard C Nice
Fecal proteomics has gained increased prominence in recent years. It can provide insights into the diagnosis and surveillance of many bowel diseases by both identifying potential biomarkers in stool samples and helping identify disease-related pathways. Fecal proteomics has already shown its potential for the discovery and validation of biomarkers for colorectal cancer screening, and the analysis of fecal microbiota by MALDI-MS for the diagnosis of a range of bowel diseases is gaining clinical acceptance. Areas covered: Based on a comprehensive analysis of the current literature, we introduce the range of sensitive and specific proteomics methods which comprise the current 'Proteomics Toolbox', explain how the integration of fecal proteomics with data processing/bioinformatics has been used for the identification of potential biomarkers for both CRC and other gut-related pathologies and analysis of the fecal microbiome, outline some of the current fecal assays in current clinical practice and introduce the concept of personalised medicine which these technologies will help inform...
May 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28341746/leveraging-sequence-based-faecal-microbial-community-survey-data-to-identify-a-composite-biomarker-for-colorectal-cancer
#17
Manasi S Shah, Todd Z DeSantis, Thomas Weinmaier, Paul J McMurdie, Julia L Cope, Adam Altrichter, Jose-Miguel Yamal, Emily B Hollister
OBJECTIVE: Colorectal cancer (CRC) is the second leading cause of cancer-associated mortality in the USA. The faecal microbiome may provide non-invasive biomarkers of CRC and indicate transition in the adenoma-carcinoma sequence. Re-analysing raw sequence and metadata from several studies uniformly, we sought to identify a composite and generalisable microbial marker for CRC. DESIGN: Raw 16S rRNA gene sequence data sets from nine studies were processed with two pipelines, (1) QIIME closed reference (QIIME-CR) or (2) a strain-specific method herein termed SS-UP (Strain Select, UPARSE bioinformatics pipeline)...
March 24, 2017: Gut
https://www.readbyqxmd.com/read/28337072/precision-metagenomics-rapid-metagenomic-analyses-for-infectious-disease-diagnostics-and-public-health-surveillance
#18
Ebrahim Afshinnekoo, Chou Chou, Noah Alexander, Sofia Ahsanuddin, Audrey N Schuetz, Christopher E Mason
Next-generation sequencing (NGS) technologies have ushered in the era of precision medicine, transforming the way we treat cancer patients and diagnose disease. Concomitantly, the advent of these technologies has created a surge of microbiome and metagenomic studies over the last decade, many of which are focused on investigating the host-gene-microbial interactions responsible for the development and spread of infectious diseases, as well as delineating their key role in maintaining health. As we continue to discover more information about the etiology of infectious diseases, the translational potential of metagenomic NGS methods for treatment and rapid diagnosis is becoming abundantly clear...
April 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/28337070/genomic-methods-and-microbiological-technologies-for-profiling-novel-and-extreme-environments-for-the-extreme-microbiome-project-xmp
#19
Scott Tighe, Ebrahim Afshinnekoo, Tara M Rock, Ken McGrath, Noah Alexander, Alexa McIntyre, Sofia Ahsanuddin, Daniela Bezdan, Stefan J Green, Samantha Joye, Sarah Stewart Johnson, Don A Baldwin, Nathan Bivens, Nadim Ajami, Joseph R Carmical, Ian Charold Herriott, Rita Colwell, Mohamed Donia, Jonathan Foox, Nick Greenfield, Tim Hunter, Jessica Hoffman, Joshua Hyman, Ellen Jorgensen, Diana Krawczyk, Jodie Lee, Shawn Levy, Natàlia Garcia-Reyero, Matthew Settles, Kelley Thomas, Felipe Gómez, Lynn Schriml, Nikos Kyrpides, Elena Zaikova, Jon Penterman, Christopher E Mason
The Extreme Microbiome Project (XMP) is a project launched by the Association of Biomolecular Resource Facilities Metagenomics Research Group (ABRF MGRG) that focuses on whole genome shotgun sequencing of extreme and unique environments using a wide variety of biomolecular techniques. The goals are multifaceted, including development and refinement of new techniques for the following: 1) the detection and characterization of novel microbes, 2) the evaluation of nucleic acid techniques for extremophilic samples, and 3) the identification and implementation of the appropriate bioinformatics pipelines...
April 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/28321234/a-review-of-bioinformatics-tools-for-bio-prospecting-from-metagenomic-sequence-data
#20
REVIEW
Despoina D Roumpeka, R John Wallace, Frank Escalettes, Ian Fotheringham, Mick Watson
The microbiome can be defined as the community of microorganisms that live in a particular environment. Metagenomics is the practice of sequencing DNA from the genomes of all organisms present in a particular sample, and has become a common method for the study of microbiome population structure and function. Increasingly, researchers are finding novel genes encoded within metagenomes, many of which may be of interest to the biotechnology and pharmaceutical industries. However, such "bioprospecting" requires a suite of sophisticated bioinformatics tools to make sense of the data...
2017: Frontiers in Genetics
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