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Microbiome bioinformatics

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https://www.readbyqxmd.com/read/29116650/microbial-biotransformations-in-the-human-distal-gut
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
https://www.readbyqxmd.com/read/28992056/a-world-of-opportunities-with-nanopore-sequencing
#9
Richard M Leggett, Matthew D Clark
Oxford Nanopore Technologies' MinION sequencer was launched in pre-release form in 2014 and represents an exciting new sequencing paradigm. The device offers multi-kilobase reads and a streamed mode of operation that allows processing of reads as they are generated. Crucially, it is an extremely compact device that is powered from the USB port of a laptop computer, enabling it to be taken out of the lab and facilitating previously impossible in-field sequencing experiments to be undertaken. Many of the initial publications concerning the platform focused on provision of tools to access and analyse the new sequence formats and then demonstrating the assembly of microbial genomes...
August 23, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28988258/moving-beyond-descriptions-of-diversity-clinical-and-research-implications-of-bacterial-imbalance-in-chronic-rhinosinusitis
#10
B Wagner Mackenzie, D W Waite, M Hoggard, M W Taylor, K Biswas, R G Douglas
Chronic rhinosinusitis (CRS) is a debilitating disease which affects 5-16% of the general population and involves long-term inflammation of the sinonasal cavity. While microbial involvement in the pathogenesis of CRS has long been suspected, the exact role of microbes remains unclear. Recent application of cultivation-independent, molecular methods has provided much new information, taking advantage of developments in both laboratory- and bioinformatics-based analyses. The aim of this mini-review is to present a variety of available bioinformatics approaches, such as data classification techniques and network analyses, with proven applications in other aspects of human microbiome health and disease research...
October 8, 2017: Rhinology
https://www.readbyqxmd.com/read/28968799/temporal-probabilistic-modeling-of-bacterial-compositions-derived-from-16s-rrna-sequencing
#11
Tarmo Äijö, Christian L Müller, Richard Bonneau
Motivation: The number of microbial and metagenomic studies has increased drastically due to advancements in next-generation sequencing-based measurement techniques. Statistical analysis and the validity of conclusions drawn from (time series) 16S rRNA and other metagenomic sequencing data is hampered by the presence of significant amount of noise and missing data (sampling zeros). Accounting uncertainty in microbiome data is often challenging due to the difficulty of obtaining biological replicates...
September 13, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28967885/assessment-of-variation-in-microbial-community-amplicon-sequencing-by-the-microbiome-quality-control-mbqc-project-consortium
#12
Rashmi Sinha, Galeb Abu-Ali, Emily Vogtmann, Anthony A Fodor, Boyu Ren, Amnon Amir, Emma Schwager, Jonathan Crabtree, Siyuan Ma, Christian C Abnet, Rob Knight, Owen White, Curtis Huttenhower
In order for human microbiome studies to translate into actionable outcomes for health, meta-analysis of reproducible data from population-scale cohorts is needed. Achieving sufficient reproducibility in microbiome research has proven challenging. We report a baseline investigation of variability in taxonomic profiling for the Microbiome Quality Control (MBQC) project baseline study (MBQC-base). Blinded specimen sets from human stool, chemostats, and artificial microbial communities were sequenced by 15 laboratories and analyzed using nine bioinformatics protocols...
November 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28961782/metacache-context-aware-classification-of-metagenomic-reads-using-minhashing
#13
André Müller, Christian Hundt, Andreas Hildebrandt, Thomas Hankeln, Bertil Schmidt
Motivation: Metagenomic shotgun sequencing studies are becoming increasingly popular with prominent examples including the sequencing of human microbiomes and diverse environments. A fundamental computational problem in this context is read classification, i.e., the assignment of each read to a taxonomic label. Due to the large number of reads produced by modern high-throughput sequencing technologies and the rapidly increasing number of available reference genomes corresponding software tools suffer from either long runtimes, large memory requirements, or low accuracy...
August 17, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28951889/functional-changes-in-the-gut-microbiome-contribute-to-transforming-growth-factor-%C3%AE-deficient-colon-cancer
#14
Scott G Daniel, Corbie L Ball, David G Besselsen, Tom Doetschman, Bonnie L Hurwitz
Colorectal cancer (CRC) is one of the most treatable cancers, with a 5-year survival rate of ~64%, yet over 50,000 deaths occur yearly in the United States. In 15% of cases, deficiency in mismatch repair leads to null mutations in transforming growth factor β (TGF-β) type II receptor, yet genotype alone is not responsible for tumorigenesis. Previous work in mice shows that disruptions in TGF-β signaling combined with Helicobacter hepaticus cause tumorigenesis, indicating a synergistic effect between genotype and microbial environment...
September 2017: MSystems
https://www.readbyqxmd.com/read/28943872/in-silico-screening-of-the-human-gut-metaproteome-identifies-th17-promoting-peptides-encrypted-in-proteins-of-commensal-bacteria
#15
Claudio Hidalgo-Cantabrana, Marco A Moro-García, Aitor Blanco-Míguez, Florentino Fdez-Riverola, Anália Lourenço, Rebeca Alonso-Arias, Borja Sánchez
Scientific studies focused on the role of the human microbiome over human health have generated billions of gigabits of genetic information during the last decade. Nowadays integration of all this information in public databases and development of pipelines allowing us to biotechnologically exploit this information are urgently needed. Prediction of the potential bioactivity of the products encoded by the human gut microbiome, or metaproteome, is the first step for identifying proteins responsible for the molecular interaction between microorganisms and the immune system...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28934286/denitrification-potential-of-the-eastern-oyster-microbiome-using-a-16s-rrna-gene-based-metabolic-inference-approach
#16
Ann Arfken, Bongkeun Song, Jeff S Bowman, Michael Piehler
The eastern oyster (Crassostrea virginica) is a foundation species providing significant ecosystem services. However, the roles of oyster microbiomes have not been integrated into any of the services, particularly nitrogen removal through denitrification. We investigated the composition and denitrification potential of oyster microbiomes with an approach that combined 16S rRNA gene analysis, metabolic inference, qPCR of the nitrous oxide reductase gene (nosZ), and N2 flux measurements. Microbiomes of the oyster digestive gland, the oyster shell, and sediments adjacent to the oyster reef were examined based on next generation sequencing (NGS) of 16S rRNA gene amplicons...
2017: PloS One
https://www.readbyqxmd.com/read/28903732/a-comparison-of-sequencing-platforms-and-bioinformatics-pipelines-for-compositional-analysis-of-the-gut-microbiome
#17
Imane Allali, Jason W Arnold, Jeffrey Roach, Maria Belen Cadenas, Natasha Butz, Hosni M Hassan, Matthew Koci, Anne Ballou, Mary Mendoza, Rizwana Ali, M Andrea Azcarate-Peril
BACKGROUND: Advancements in Next Generation Sequencing (NGS) technologies regarding throughput, read length and accuracy had a major impact on microbiome research by significantly improving 16S rRNA amplicon sequencing. As rapid improvements in sequencing platforms and new data analysis pipelines are introduced, it is essential to evaluate their capabilities in specific applications. The aim of this study was to assess whether the same project-specific biological conclusions regarding microbiome composition could be reached using different sequencing platforms and bioinformatics pipelines...
September 13, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28875147/protected-sampling-is-preferable-in-bronchoscopic-studies-of-the-airway-microbiome
#18
Rune Grønseth, Christine Drengenes, Harald G Wiker, Solveig Tangedal, Yaxin Xue, Gunnar Reksten Husebø, Øistein Svanes, Sverre Lehmann, Marit Aardal, Tuyen Hoang, Tharmini Kalananthan, Einar Marius Hjellestad Martinsen, Elise Orvedal Leiten, Marianne Aanerud, Eli Nordeide, Ingvild Haaland, Inge Jonassen, Per Bakke, Tomas Eagan
The aim was to evaluate susceptibility of oropharyngeal contamination with various bronchoscopic sampling techniques. 67 patients with obstructive lung disease and 58 control subjects underwent bronchoscopy with small-volume lavage (SVL) through the working channel, protected bronchoalveolar lavage (PBAL) and bilateral protected specimen brush (PSB) sampling. Subjects also provided an oral wash (OW) sample, and negative control samples were gathered for each bronchoscopy procedure. DNA encoding bacterial 16S ribosomal RNA was sequenced and bioinformatically processed to cluster into operational taxonomic units (OTU), assign taxonomy and obtain measures of diversity...
July 2017: ERJ Open Research
https://www.readbyqxmd.com/read/28854168/commensal-bacteria-make-gpcr-ligands-that-mimic-human-signalling-molecules
#19
COMPARATIVE STUDY
Louis J Cohen, Daria Esterhazy, Seong-Hwan Kim, Christophe Lemetre, Rhiannon R Aguilar, Emma A Gordon, Amanda J Pickard, Justin R Cross, Ana B Emiliano, Sun M Han, John Chu, Xavier Vila-Farres, Jeremy Kaplitt, Aneta Rogoz, Paula Y Calle, Craig Hunter, J Kipchirchir Bitok, Sean F Brady
Commensal bacteria are believed to have important roles in human health. The mechanisms by which they affect mammalian physiology remain poorly understood, but bacterial metabolites are likely to be key components of host interactions. Here we use bioinformatics and synthetic biology to mine the human microbiota for N-acyl amides that interact with G-protein-coupled receptors (GPCRs). We found that N-acyl amide synthase genes are enriched in gastrointestinal bacteria and the lipids that they encode interact with GPCRs that regulate gastrointestinal tract physiology...
September 7, 2017: Nature
https://www.readbyqxmd.com/read/28845973/human-microbiome-inspired-antibiotics-with-improved-%C3%AE-lactam-synergy-against-mdr-staphylococcus-aureus
#20
John Chu, Xavier Vila-Farres, Daigo Inoyama, Ricardo Gallardo-Macias, Mark Jaskowski, Shruthi Satish, Joel S Freundlich, Sean F Brady
The flippase MurJ is responsible for transporting the cell wall intermediate lipid II from the cytoplasm to the outside of the cell. While essential for the survival of bacteria, it remains an underexploited target for antibacterial therapy. The humimycin antibiotics are lipid II flippase (MurJ) inhibitors that were synthesized on the basis of bioinformatic predictions derived from secondary metabolite gene clusters found in the human microbiome. Here, we describe an SAR campaign around humimycin A that produced humimycin 17S...
September 11, 2017: ACS Infectious Diseases
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