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Microbiome bioinformatics

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https://www.readbyqxmd.com/read/27884202/extending-colonic-mucosal-microbiome-analysis-assessment-of-colonic-lavage-as-a-proxy-for-endoscopic-colonic-biopsies
#1
Euan Watt, Matthew R Gemmell, Susan Berry, Mark Glaire, Freda Farquharson, Petra Louis, Graeme I Murray, Emad El-Omar, Georgina L Hold
BACKGROUND: Sequencing-based analysis has become a well-established approach to deciphering the composition of the gut microbiota. However, due to the complexity of accessing sufficient material from colonoscopic biopsy samples, most studies have focused on faecal microbiota analysis, even though it is recognised that differences exist between the microbial composition of colonic biopsies and faecal samples. We determined the suitability of colonic lavage samples to see if it had comparable microbial diversity composition to colonic biopsies as they are without the limitations associated with sample size...
November 25, 2016: Microbiome
https://www.readbyqxmd.com/read/27881416/metagenomics-of-two-severe-foodborne-outbreaks-provides-diagnostic-signatures-and-signs-of-co-infection-not-attainable-by-traditional-methods
#2
Andrew D Huang, Chengwei Luo, Angela Pena-Gonzalez, Michael R Weigand, Cheryl Tarr, Konstantinos T Konstantinidis
: Diagnostic testing for foodborne pathogens relies on culture-based techniques that are not rapid enough for real-time disease surveillance and do not give a quantitative picture of pathogen abundance or the response of the natural microbiome. Powerful sequence-based, culture-independent approaches such as shotgun metagenomics could sidestep these limitations, and potentially reveal a pathogen-specific signature on the microbiome that would have implications not only for diagnostics but also for better understanding disease progression and pathogen ecology...
November 23, 2016: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27869143/genome-mining-unveils-widespread-natural-product-biosynthetic-capacity-in-human-oral-microbe-streptococcus-mutans
#3
Liwei Liu, Tingting Hao, Zhoujie Xie, Geoff P Horsman, Yihua Chen
Streptococcus mutans is a major pathogen causing human dental caries. As a Gram-positive bacterium with a small genome (about 2 Mb) it is considered a poor source of natural products. Due to a recent explosion in genomic data available for S. mutans strains, we were motivated to explore the natural product production potential of this organism. Bioinformatic characterization of 169 publically available genomes of S. mutans from human dental caries revealed a surprisingly rich source of natural product biosynthetic gene clusters...
November 21, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27861983/genomic-and-metagenomic-technologies-to-explore-the-antibiotic-resistance-mobilome
#4
José L Martínez, Teresa M Coque, Val F Lanza, Fernando de la Cruz, Fernando Baquero
Antibiotic resistance is a relevant problem for human health that requires global approaches to establish a deep understanding of the processes of acquisition, stabilization, and spread of resistance among human bacterial pathogens. Since natural (nonclinical) ecosystems are reservoirs of resistance genes, a health-integrated study of the epidemiology of antibiotic resistance requires the exploration of such ecosystems with the aim of determining the role they may play in the selection, evolution, and spread of antibiotic resistance genes, involving the so-called resistance mobilome...
November 10, 2016: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/27861551/genomes-of-gardnerella-strains-reveal-an-abundance-of-prophages-within-the-bladder-microbiome
#5
Kema Malki, Jason W Shapiro, Travis K Price, Evann E Hilt, Krystal Thomas-White, Trina Sircar, Amy B Rosenfeld, Gina Kuffel, Michael J Zilliox, Alan J Wolfe, Catherine Putonti
Bacterial surveys of the vaginal and bladder human microbiota have revealed an abundance of many similar bacterial taxa. As the bladder was once thought to be sterile, the complex interactions between microbes within the bladder have yet to be characterized. To initiate this process, we have begun sequencing isolates, including the clinically relevant genus Gardnerella. Herein, we present the genomic sequences of four Gardnerella strains isolated from the bladders of women with symptoms of urgency urinary incontinence; these are the first Gardnerella genomes produced from this niche...
2016: PloS One
https://www.readbyqxmd.com/read/27856569/personal-microbiomes-and-next-generation-sequencing-for-laboratory-based-education
#6
Mark R Hartman, Kristin T Harrington, Candice M Etson, Matthew B Fierman, Donna K Slonim, David R Walt
Sequencing and bioinformatics technologies have advanced rapidly in recent years, driven largely by developments in next-generation sequencing (NGS) technology. Given the increasing importance of these advances, there is a growing need to incorporate concepts and practices relating to NGS into undergraduate and high school science curricula. We believe that direct access to sequencing and bioinformatics will improve the ability of students to understand the information obtained through these increasingly ubiquitous research tools...
November 16, 2016: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/27842515/evaluation-of-pacbio-sequencing-for-full-length-bacterial-16s-rrna-gene-classification
#7
Josef Wagner, Paul Coupland, Hilary P Browne, Trevor D Lawley, Suzanna C Francis, Julian Parkhill
BACKGROUND: Currently, bacterial 16S rRNA gene analyses are based on sequencing of individual variable regions of the 16S rRNA gene (Kozich, et al Appl Environ Microbiol 79:5112-5120, 2013).This short read approach can introduce biases. Thus, full-length bacterial 16S rRNA gene sequencing is needed to reduced biases. A new alternative for full-length bacterial 16S rRNA gene sequencing is offered by PacBio single molecule, real-time (SMRT) technology. The aim of our study was to validate PacBio P6 sequencing chemistry using three approaches: 1) sequencing the full-length bacterial 16S rRNA gene from a single bacterial species Staphylococcus aureus to analyze error modes and to optimize the bioinformatics pipeline; 2) sequencing the full-length bacterial 16S rRNA gene from a pool of 50 different bacterial colonies from human stool samples to compare with full-length bacterial 16S rRNA capillary sequence; and 3) sequencing the full-length bacterial 16S rRNA genes from 11 vaginal microbiome samples and compare with in silico selected bacterial 16S rRNA V1V2 gene region and with bacterial 16S rRNA V1V2 gene regions sequenced using the Illumina MiSeq...
November 14, 2016: BMC Microbiology
https://www.readbyqxmd.com/read/27825829/metagenomics-probing-pollutant-fate-in-natural-and-engineered-ecosystems
#8
REVIEW
Emna Bouhajja, Spiros N Agathos, Isabelle F George
Polluted environments are a reservoir of microbial species able to degrade or to convert pollutants to harmless compounds. The proper management of microbial resources requires a comprehensive characterization of their genetic pool to assess the fate of contaminants and increase the efficiency of bioremediation processes. Metagenomics offers appropriate tools to describe microbial communities in their whole complexity without lab-based cultivation of individual strains. After a decade of use of metagenomics to study microbiomes, the scientific community has made significant progress in this field...
November 5, 2016: Biotechnology Advances
https://www.readbyqxmd.com/read/27822553/mockrobiota-a-public-resource-for-microbiome-bioinformatics-benchmarking
#9
Nicholas A Bokulich, Jai Ram Rideout, William G Mercurio, Arron Shiffer, Benjamin Wolfe, Corinne F Maurice, Rachel J Dutton, Peter J Turnbaugh, Rob Knight, J Gregory Caporaso
Mock communities are an important tool for validating, optimizing, and comparing bioinformatics methods for microbial community analysis. We present mockrobiota, a public resource for sharing, validating, and documenting mock community data resources, available at http://caporaso-lab.github.io/mockrobiota/. The materials contained in mockrobiota include data set and sample metadata, expected composition data (taxonomy or gene annotations or reference sequences for mock community members), and links to raw data (e...
September 2016: MSystems
https://www.readbyqxmd.com/read/27822515/open-source-sequence-clustering-methods-improve-the-state-of-the-art
#10
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/27793585/methodologies-for-probing-the-metatranscriptome-of-grassland-soil
#11
Aaron Garoutte, Erick Cardenas, James Tiedje, Adina Howe
Metatranscriptomics provides an opportunity to identify active microbes and expressed genes in complex soil communities in response to particular conditions. Currently, there are a limited number of soil metatranscriptome studies to provide guidance for using this approach in this challenging matrix. Hence, we evaluated the technical challenges of applying soil metatranscriptomics to a highly diverse, low activity natural system. We used a non-targeted rRNA removal approach, duplex nuclease specific (DSN) normalization, to generate a metatranscriptomic library from field collected soil supporting a perennial grass, Miscanthus x giganteus (a biofuel crop), and evaluated its ability to provide insight into its active community members and their expressed protein-coding genes...
October 25, 2016: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/27762069/an-introduction-to-microbiome-analysis-for-human-biology-applications
#12
Katherine R Amato
Research examining the gut microbiota is currently exploding, and results are providing new perspectives on human biology. Factors such as host diet and physiology influence the composition and function of the gut microbiota, which in turn affects human nutrition, health, and behavior via interactions with metabolism, the immune system, and the brain. These findings represent an exciting new twist on familiar topics, and as a result, gut microbiome research is likely to provide insight into unresolved biological mechanisms driving human health...
October 20, 2016: American Journal of Human Biology: the Official Journal of the Human Biology Council
https://www.readbyqxmd.com/read/27748750/discovery-of-mrsa-active-antibiotics-using-primary-sequence-from-the-human-microbiome
#13
John Chu, Xavier Vila-Farres, Daigo Inoyama, Melinda Ternei, Louis J Cohen, Emma A Gordon, Boojala Vijay B Reddy, Zachary Charlop-Powers, Henry A Zebroski, Ricardo Gallardo-Macias, Mark Jaskowski, Shruthi Satish, Steven Park, David S Perlin, Joel S Freundlich, Sean F Brady
Here we present a natural product discovery approach, whereby structures are bioinformatically predicted from primary sequence and produced by chemical synthesis (synthetic-bioinformatic natural products, syn-BNPs), circumventing the need for bacterial culture and gene expression. When we applied the approach to nonribosomal peptide synthetase gene clusters from human-associated bacteria, we identified the humimycins. These antibiotics inhibit lipid II flippase and potentiate β-lactam activity against methicillin-resistant Staphylococcus aureus in mice, potentially providing a new treatment regimen...
December 2016: Nature Chemical Biology
https://www.readbyqxmd.com/read/27712009/broad-phylogeny-and-functionality-of-cellulosomal-components-in-the-bovine-rumen-microbiome
#14
Lizi Bensoussan, Sarah Moraïs, Bareket Dassa, Nir Friedman, Bernard Henrissat, Vincent Lombard, Edward A Bayer, Itzhak Mizrahi
The cellulosome is an extracellular multi-enzyme complex that is considered one of the most efficient plant cell wall-degrading strategies devised by nature. Its unique modular architecture, achieved by high affinity and specific interaction between protein modules (cohesins and dockerins) enables formation of various enzyme combinations. Extensive research has been dedicated to the mechanistic nature of the cellulosome complex. Nevertheless, little is known regarding its distribution and abundance among microbes in natural plant fiber-rich environments...
October 6, 2016: Environmental Microbiology
https://www.readbyqxmd.com/read/27698620/the-hoops-hopes-and-hypes-of-human-microbiome-research
#15
Elisabeth M Bik
Recent developments in sequencing methods and bioinformatics analysis tools have greatly enabled the culture-independent analysis of complex microbial communities associated with environmental samples, plants, and animals. This has led to a spectacular increase in the number of studies on both membership and functionalities of these hitherto invisible worlds, in particular those of the human microbiome. The wide variety in available microbiome tools and platforms can be overwhelming, and making sound conclusions from scientific research can be challenging...
September 2016: Yale Journal of Biology and Medicine
https://www.readbyqxmd.com/read/27697111/probing-the-diversity-of-healthy-oral-microbiome-with-bioinformatics-approaches
#16
Ji-Hoi Moon, Jae-Hyung Lee
Human oral cavity contains a highly personalized microbiome that is essential to maintaining health but capable of causing oral and systemic diseases. Thus, an in-depth definition of "healthy oral microbiome" is critical to understanding variations in disease states from preclinical conditions and disease onset through progressive states of disease. With rapid advances in DNA sequencing and analytical technologies, population-based studies have documented the ranges and diversity of both taxonomic compositions and functional potentials observed in the oral microbiome in healthy individuals...
September 29, 2016: BMB Reports
https://www.readbyqxmd.com/read/27694142/uncoupling-of-mucosal-gene-regulation-mrna-splicing-and-adherent-microbiota-signatures-in-inflammatory-bowel-disease
#17
Robert Häsler, Raheleh Sheibani-Tezerji, Anupam Sinha, Matthias Barann, Ateequr Rehman, Daniela Esser, Konrad Aden, Carolin Knecht, Berenice Brandt, Susanna Nikolaus, Sascha Schäuble, Christoph Kaleta, Andre Franke, Christoph Fretter, Werner Müller, Marc-Thorsten Hütt, Michael Krawczak, Stefan Schreiber, Philip Rosenstiel
OBJECTIVE: An inadequate host response to the intestinal microbiota likely contributes to the manifestation and progression of human inflammatory bowel disease (IBD). However, molecular approaches to unravelling the nature of the defective crosstalk and its consequences for intestinal metabolic and immunological networks are lacking. We assessed the mucosal transcript levels, splicing architecture and mucosa-attached microbial communities of patients with IBD to obtain a comprehensive view of the underlying, hitherto poorly characterised interactions, and how these are altered in IBD...
September 30, 2016: Gut
https://www.readbyqxmd.com/read/27687690/samsa-a-comprehensive-metatranscriptome-analysis-pipeline
#18
Samuel T Westreich, Ian Korf, David A Mills, Danielle G Lemay
BACKGROUND: Although metatranscriptomics-the study of diverse microbial population activity based on RNA-seq data-is rapidly growing in popularity, there are limited options for biologists to analyze this type of data. Current approaches for processing metatranscriptomes rely on restricted databases and a dedicated computing cluster, or metagenome-based approaches that have not been fully evaluated for processing metatranscriptomic datasets. We created a new bioinformatics pipeline, designed specifically for metatranscriptome dataset analysis, which runs in conjunction with Metagenome-RAST (MG-RAST) servers...
September 29, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27634945/reference-point-insensitive-molecular-data-analysis
#19
M Altenbuchinger, T Rehberg, H U Zacharias, F Stämmler, K Dettmer, D Weber, A Hiergeist, A Gessner, E Holler, P J Oefner, R Spang
MOTIVATION: In biomedicine, every molecular measurement is relative to a reference point, like a fixed aliquot of RNA extracted from a tissue, a defined number of blood cells, or a defined volume of biofluid. Reference points are often chosen for practical reasons. For example, we might want to assess the metabolome of a diseased organ but can only measure metabolites in blood or urine. In this case the observable data only indirectly reflects the disease state. The statistical implications of these discrepancies in reference points have not yet been discussed...
September 15, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27571759/an-assessment-of-us-microbiome-research
#20
Elizabeth Stulberg, Deborah Fravel, Lita M Proctor, David M Murray, Jonathan LoTempio, Linda Chrisey, Jay Garland, Kelly Goodwin, Joseph Graber, M Camille Harris, Scott Jackson, Michael Mishkind, D Marshall Porterfield, Angela Records
Genome-enabled technologies have supported a dramatic increase in our ability to study microbial communities in environments and hosts. Taking stock of previously funded microbiome research can help to identify common themes, under-represented areas and research priorities to consider moving forward. To assess the status of US microbiome research, a team of government scientists conducted an analysis of federally funded microbiome research. Microbiomes were defined as host-, ecosystem- or habitat-associated communities of microorganisms, and microbiome research was defined as those studies that emphasize community-level analyses using 'omics technologies...
2016: Nature Microbiology
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