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Microbiome bioinformatics

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https://www.readbyqxmd.com/read/29312814/on-revealing-the-gene-targets-of-ebola-virus-micrornas-involved-in-the-human-skin-microbiome
#1
Pei-Chun Hsu, Bin-Hao Chiou, Chun-Ming Huang
Ebola virus, a negative-sense single-stranded RNA virus, causes severe viral hemorrhagic fever and has a high mortality rate. Histopathological and immunopathological analyses of Ebola virus have revealed that histopathological changes in skin tissue are associated with various degrees of endothelial cell swelling and necrosis. The interactions of microbes within or on a host are a crucial for the skin immune shield. The discovery of microRNAs (miRNAs) in Ebola virus implies that immune escape, endothelial cell rupture, and tissue dissolution during Ebola virus infection are a result of the effects of Ebola virus miRNAs...
2018: PeerJ
https://www.readbyqxmd.com/read/29281673/taxonomic-differences-of-gut-microbiomes-drive-cellulolytic-enzymatic-potential-within-hind-gut-fermenting-mammals
#2
Emma C L Finlayson-Trick, Landon J Getz, Patrick D Slaine, Mackenzie Thornbury, Emily Lamoureux, Jamie Cook, Morgan G I Langille, Lois E Murray, Craig McCormick, John R Rohde, Zhenyu Cheng
Host diet influences the diversity and metabolic activities of the gut microbiome. Previous studies have shown that the gut microbiome provides a wide array of enzymes that enable processing of diverse dietary components. Because the primary diet of the porcupine, Erethizon dorsatum, is lignified plant material, we reasoned that the porcupine microbiome would be replete with enzymes required to degrade lignocellulose. Here, we report on the bacterial composition in the porcupine microbiome using 16S rRNA sequencing and bioinformatics analysis...
2017: PloS One
https://www.readbyqxmd.com/read/29274958/mining-metagenomic-and-metatranscriptomic-data-for-clues-about-microbial-metabolic-functions-in-ruminants
#3
Fuyong Li, Andre L A Neves, Bibaswan Ghoshal, Le Luo Guan
Metagenomics and metatranscriptomics can capture the whole genome and transcriptome repertoire of microorganisms through sequencing total DNA/RNA from various environmental samples, providing both taxonomic and functional information with high resolution. The unique and complex rumen microbial ecosystem is receiving great research attention because the rumen microbiota coevolves with the host and equips ruminants with the ability to convert cellulosic plant materials to high-protein products for human consumption...
December 20, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/29250787/metagenomics-in-pooled-plasma-with-identification-of-potential-emerging-infectious-pathogens
#4
Min Xu, Yashan Yang, Ya Zhou, Zhiyang Liu, Yu Liu, Miao He
BACKGROUND: Many emerging infectious pathogens are well known for existing in healthy blood donors and could be transmitted via blood transfusion or plasma derivatives usage. Therefore, there is an urgent need to discover the pathogens in qualified blood donation to avoid potential threats to blood safety. STUDY DESIGN AND METHODS: The objective of this study was to investigate the microbiome that existed in pooled plasma from different manufacturers in Chengdu and Guiyang...
December 17, 2017: Transfusion
https://www.readbyqxmd.com/read/29242834/novel-its1-fungal-primers-for-characterization-of-the-mycobiome
#5
Mykhaylo Usyk, Christine P Zolnik, Hitesh Patel, Michael H Levi, Robert D Burk
Studies of the human microbiome frequently omit characterization of fungal communities (the mycobiome), which limits our ability to investigate how fungal communities influence human health. The internal transcribed spacer 1 (ITS1) region of the eukaryotic ribosomal cluster has features allowing for wide taxonomic coverage and has been recognized as a suitable barcode region for species-level identification of fungal organisms. We developed custom ITS1 primer sets using iterative alignment refinement. Primer performance was evaluated using in silico testing and experimental testing of fungal cultures and human samples...
November 2017: MSphere
https://www.readbyqxmd.com/read/29212440/constax-a-tool-for-improved-taxonomic-resolution-of-environmental-fungal-its-sequences
#6
Kristi Gdanetz, Gian Maria Niccolò Benucci, Natalie Vande Pol, Gregory Bonito
BACKGROUND: One of the most crucial steps in high-throughput sequence-based microbiome studies is the taxonomic assignment of sequences belonging to operational taxonomic units (OTUs). Without taxonomic classification, functional and biological information of microbial communities cannot be inferred or interpreted. The internal transcribed spacer (ITS) region of the ribosomal DNA is the conventional marker region for fungal community studies. While bioinformatics pipelines that cluster reads into OTUs have received much attention in the literature, less attention has been given to the taxonomic classification of these sequences, upon which biological inference is dependent...
December 6, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29186317/computational-profiling-of-the-gut-brain-axis-microflora-dysbiosis-insights-to-neurological-disorders
#7
Nikolas Dovrolis, George Kolios, George M Spyrou, Ioanna Maroulakou
Almost 2500 years after Hippocrates' observations on health and its direct association to the gastrointestinal tract, a paradigm shift has recently occurred, making the gut and its symbionts (bacteria, fungi, archaea and viruses) a point of convergence for studies. It is nowadays well established that the gut microflora's compositional diversity regulates via its genes (the microbiome) the host's health and provides preliminary insights into disease progression and regulation. The microbiome's involvement is evident in immunological and physiological studies that link changes in its biodiversity to its contributions to the host's phenotype but also in neurological investigations, substantiating the aptly named gut-brain axis...
November 27, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29186315/resources-and-tools-for-the-high-throughput-multi-omic-study-of-intestinal-microbiota
#8
Aitor Blanco-Míguez, Florentino Fdez-Riverola, Borja Sánchez, Anália Lourenço
The human gut microbiome impacts several aspects of human health and disease, including digestion, drug metabolism and the propensity to develop various inflammatory, autoimmune and metabolic diseases. Many of the molecular processes that play a role in the activity and dynamics of the microbiota go beyond species and genic composition and thus, their understanding requires advanced bioinformatics support. This article aims to provide an up-to-date view of the resources and software tools that are being developed and used in human gut microbiome research, in particular data integration and systems-level analysis efforts...
November 27, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29176472/the-omes-of-inflammatory-bowel-disease-a-primer-for-clinicians
#9
Joseph A Picoraro, Neal S LeLeiko
Recent advances in high-throughput laboratory technologies and bioinformatics tools are redefining how we view inflammatory bowel disease (IBD). Instead of two diseases we now see a diverse set of molecular subtypes. Large scale investigation of the genome, exome, transcriptome, proteome, metabolome, microbiome, and epigenome are providing transformative insights into the pathophysiology of IBD, with the promise of accurately predicting prognosis and targeting therapy. Understanding these tools and their application is crucial to navigating the molecular era of IBD...
November 22, 2017: Journal of Pediatric Gastroenterology and Nutrition
https://www.readbyqxmd.com/read/29172724/distribution-and-diversity-of-ocular-microbial-communities-in-diabetic-patients-compared-with-healthy-subjects
#10
Baknoon Ham, Hyung Bin Hwang, Sang Hoon Jung, Sungyul Chang, Kui Dong Kang, Man Jae Kwon
PURPOSE: The aim of this study was to identify differences in the major (core vs. variable) microbial genera of human subjects with and without diabetes. METHODS: Bacterial 16S rRNA genes obtained from conjunctival swabs of 19 healthy subjects and 30 diabetic patients were sequenced using the Illumina MiSeq platform, and the sequencing data were analyzed using QIIME 1.9.1. To elucidate the microbial diversity in the ocular surface (OS), test programs from various bioinformatics domains were used...
November 27, 2017: Current Eye Research
https://www.readbyqxmd.com/read/29157945/food-allergy-a-review-and-update-on-epidemiology-pathogenesis-diagnosis-prevention-and-management
#11
Scott H Sicherer, Hugh A Sampson
This review provides general information to serve as a primer for those embarking on understanding food allergy and also details advances and updates in epidemiology, pathogenesis, diagnosis and treatment that have occurred over the four years since our last comprehensive review. Although firm prevalence data are lacking, there is a strong impression that food allergy has increased, and rates as high as ∼10% have been documented. Genetic, epigenetic and environmental risk factors are being increasingly elucidated, opening the potential for improved prevention and treatment strategies targeted to those at risk...
November 17, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/29152146/breast-tissue-oral-and-urinary-microbiomes-in-breast-cancer
#12
Hannah Wang, Jessica Altemus, Farshad Niazi, Holly Green, Benjamin C Calhoun, Charles Sturgis, Stephen R Grobmyer, Charis Eng
It has long been proposed that the gut microbiome contributes to breast carcinogenesis by modifying systemic estrogen levels. This is often cited as a possible mechanism linking breast cancer and high-fat, low-fiber diets as well as antibiotic exposure, associations previously identified in population-based studies. More recently, a distinct microbiome has been identified within breast milk and tissue, but few studies have characterized differences in the breast tissue microbiota of patients with and without cancer, and none have investigated distant body-site microbiomes outside of the gut...
October 20, 2017: Oncotarget
https://www.readbyqxmd.com/read/29116650/microbial-biotransformations-in-the-human-distal-gut
#13
REVIEW
Elisabeth M Bik, Juan A Ugalde, Jon Cousins, Audrey D Goddard, Jessica Richman, Zachary S Apte
The human distal gut is home to a rich and dense microbial community with representatives of all three domains of life which are intricately connected with our physiology and health. The combined genomes of these microbes, collectively called the human microbiome, vastly expand the metabolic capacities of our own genome, allowing us to break down and extract energy from dietary compounds that human enzymes cannot digest. In addition, the variable composition of these communities and their biotransformations might explain inter-individual differences in toxicities, tolerances, and efficacies for certain drugs...
November 8, 2017: British Journal of Pharmacology
https://www.readbyqxmd.com/read/29112885/commensal-koch-s-postulates-establishing-causation-in-human-microbiota-research
#14
REVIEW
B Anne Neville, Samuel C Forster, Trevor D Lawley
Advances in high-throughput sequencing technologies and the development of sophisticated bioinformatics analysis methods, algorithms, and pipelines to handle the large amounts of data generated have driven the field of human microbiome research forward. This specialist knowledge has been crucial to thoroughly mine the human gut microbiota, particularly in the absence of methods for the routine cultivation of most enteric microorganisms. In recent years, however, significant efforts have been made to address the 'great plate count anomaly' and to overcome the barriers to cultivation of the fastidious and mostly strictly anaerobic bacteria that reside in the human gut...
November 4, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/29106667/microbiomedb-a-systems-biology-platform-for-integrating-mining-and-analyzing-microbiome-experiments
#15
Francislon S Oliveira, John Brestelli, Shon Cade, Jie Zheng, John Iodice, Steve Fischer, Cristina Aurrecoechea, Jessica C Kissinger, Brian P Brunk, Christian J Stoeckert, Gabriel R Fernandes, David S Roos, Daniel P Beiting
MicrobiomeDB (http://microbiomeDB.org) is a data discovery and analysis platform that empowers researchers to fully leverage experimental variables to interrogate microbiome datasets. MicrobiomeDB was developed in collaboration with the Eukaryotic Pathogens Bioinformatics Resource Center (http://EuPathDB.org) and leverages the infrastructure and user interface of EuPathDB, which allows users to construct in silico experiments using an intuitive graphical 'strategy' approach. The current release of the database integrates microbial census data with sample details for nearly 14 000 samples originating from human, animal and environmental sources, including over 9000 samples from healthy human subjects in the Human Microbiome Project (http://portal...
November 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29106611/mvoc-2-0-a-database-of-microbial-volatiles
#16
Marie C Lemfack, Bjoern-Oliver Gohlke, Serge M T Toguem, Saskia Preissner, Birgit Piechulla, Robert Preissner
Metabolic capabilities of microorganisms include the production of secondary metabolites (e.g. antibiotics). The analysis of microbial volatile organic compounds (mVOCs) is an emerging research field with huge impact on medical, agricultural and biotechnical applied and basic science. The mVOC database (v1) has grown with microbiome research and integrated species information with data on emitted volatiles. Here, we present the mVOC 2.0 database with about 2000 compounds from almost 1000 species and new features to work with the database...
November 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29098532/microbial-community-and-ovine-host-response-varies-with-early-and-late-stages-of-haemonchus-contortus-infection
#17
Saeed El-Ashram, Ibrahim Al Nasr, Fathi Abouhajer, Maged El-Kemary, Guangping Huang, Güngör Dinçel, Rashid Mehmood, Min Hu, Xun Suo
The interactions between gastric microbiota, ovine host, and Haemonchus contortus portray the ovine gastric environment as a complex ecosystem, where all factors play a pertinent role in fine-tuning each other and in haemeostasis. We delineated the impact of early and late Haemonchus infection on abomasal and ruminal microbial community, as well as the ovine host. Twelve, parasite-naive lambs were divided into four groups, 7 days post-infection (dpi) and time-matched uninfected-control groups; 50 dpi and time-matched uninfected control groups were used for the experiment...
December 2017: Veterinary Research Communications
https://www.readbyqxmd.com/read/29071712/the-role-of-the-microbiome-in-psoriasis-moving-from-disease-description-to-treatment-prediction
#18
REVIEW
E A Langan, C E M Griffiths, W Solbach, J K Knobloch, D Zillikens, D Thaçi
With several million microbes per cm(2) of skin, the task of mapping the physiological cutaneous microbiome is enormous. Indeed, the reliance on bacterial culture to identify cutaneous bacterial communities has led to a systematic under-appreciation of cutaneous microbial diversity, potentially limiting our understanding of common inflammatory skin diseases including psoriasis. However, based heavily on developments in molecular biology and bioinformatics, including next generation sequencing, the last decade has witnessed a marked increase in our understanding of the extent and composition of the cutaneous microbiome...
October 26, 2017: British Journal of Dermatology
https://www.readbyqxmd.com/read/29040451/an-omnibus-test-for-differential-distribution-analysis-of-microbiome-sequencing-data
#19
Jun Chen, Emily King, Rebecca Deek, Zhi Wei, Yue Yu, Diane Grill, Karla Ballman
Motivation: One objective of human microbiome studies is to identify differentially abundant microbes across biological conditions. Previous statistical methods focus on detecting the shift in the abundance and/or prevalence of the microbes and treat the dispersion (spread of the data) as a nuisance. These methods also assume that the dispersion is the same across conditions, an assumption which may not hold in presence of sample heterogeneity. Moreover, the widespread outliers in the microbiome sequencing data make existing parametric models not overly robust...
October 12, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29018846/antibiotics-and-specialized-metabolites-from-the-human-microbiota
#20
REVIEW
Walaa K Mousa, Bilal Athar, Nishanth J Merwin, Nathan A Magarvey
Covering: 2000 to 2017Decades of research on human microbiota have revealed much of their taxonomic diversity and established their direct link to health and disease. However, the breadth of bioactive natural products secreted by our microbial partners remains unknown. Of particular interest are antibiotics produced by our microbiota to ward off invasive pathogens. Members of the human microbiota exclusively produce evolved small molecules with selective antimicrobial activity against human pathogens. Herein, we expand upon the current knowledge concerning antibiotics derived from human microbiota and their distribution across body sites...
November 15, 2017: Natural Product Reports
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