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Microbial bioinformatics

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https://www.readbyqxmd.com/read/28932815/a-multicenter-study-to-evaluate-the-performance-of-high-throughput-sequencing-for-virus-detection
#1
Arifa S Khan, Siemon H S Ng, Olivier Vandeputte, Aisha Aljanahi, Avisek Deyati, Jean-Pol Cassart, Robert L Charlebois, Lanyn P Taliaferro
The capability of high-throughput sequencing (HTS) for detection of known and unknown viruses makes it a powerful tool for broad microbial investigations, such as evaluation of novel cell substrates that may be used for the development of new biological products. However, like any new assay, regulatory applications of HTS need method standardization. Therefore, our three laboratories initiated a study to evaluate performance of HTS for potential detection of viral adventitious agents by spiking model viruses in different cellular matrices to mimic putative materials for manufacturing of biologics...
September 2017: MSphere
https://www.readbyqxmd.com/read/28930150/detection-of-bacterial-pathogens-from-broncho-alveolar-lavage-by-next-generation-sequencing
#2
Stefano Leo, Nadia Gaïa, Etienne Ruppé, Stephane Emonet, Myriam Girard, Vladimir Lazarevic, Jacques Schrenzel
The applications of whole-metagenome shotgun sequencing (WMGS) in routine clinical analysis are still limited. A combination of a DNA extraction procedure, sequencing, and bioinformatics tools is essential for the removal of human DNA and for improving bacterial species identification in a timely manner. We tackled these issues with a broncho-alveolar lavage (BAL) sample from an immunocompromised patient who had developed severe chronic pneumonia. We extracted DNA from the BAL sample with protocols based either on sequential lysis of human and bacterial cells or on the mechanical disruption of all cells...
September 20, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28924496/challenging-a-bioinformatic-tool-s-ability-to-detect-microbial-contaminants-using-in-silico-whole-genome-sequencing-data
#3
Nathan D Olson, Justin M Zook, Jayne B Morrow, Nancy J Lin
High sensitivity methods such as next generation sequencing and polymerase chain reaction (PCR) are adversely impacted by organismal and DNA contaminants. Current methods for detecting contaminants in microbial materials (genomic DNA and cultures) are not sensitive enough and require either a known or culturable contaminant. Whole genome sequencing (WGS) is a promising approach for detecting contaminants due to its sensitivity and lack of need for a priori assumptions about the contaminant. Prior to applying WGS, we must first understand its limitations for detecting contaminants and potential for false positives...
2017: PeerJ
https://www.readbyqxmd.com/read/28903732/a-comparison-of-sequencing-platforms-and-bioinformatics-pipelines-for-compositional-analysis-of-the-gut-microbiome
#4
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/28900280/metagenomic-insight-into-the-microbial-networks-and-metabolic-mechanism-in-anaerobic-digesters-for-food-waste-by-incorporating-activated-carbon
#5
Jingxin Zhang, Liwei Mao, Le Zhang, Kai-Chee Loh, Yanjun Dai, Yen Wah Tong
Powdered activated carbon (AC) is commonly used as an effective additive to enhance anaerobic digestion (AD), but little is known about how the metabolic pathways resulting from adding AC change the microbial association network and enhance food waste treatment. In this work, the use of AC in an anaerobic digestion system for food waste was explored. Using bioinformatics analysis, taxonomic trees and the KEGG pathway analysis, changes in microbial network and biometabolic pathways were tracked. The overall effect of these changes were used to explain and validate improved digestion performance...
September 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28895366/-purification-identification-and-characterization-of-an-anti-microbial-hexapeptide-from-sus-scrofa-lysozyme
#6
Dewei Zhu, Guolin Cai, Jian Lu
Sus scrofa lysozyme (SSL) was digested by different proteases to find peptides with enhanced antibacterial activity against gram-negative bacteria. Hydrolysate with the highest anti-bacterial activity was loaded onto a gel filtration chromatography column followed by a reversed-phase one. The obtained substance was identified by liquid chromatography-mass spectrometry, synthesized to test its antibacterial spectrum and analyzed for bioinformatics. The hydrolysate of trypsin showed the highest antibacterial activity...
June 25, 2017: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
https://www.readbyqxmd.com/read/28892494/infections-by-human-gastrointestinal-helminths-are-associated-with-changes-in-faecal-microbiota-diversity-and-composition
#7
Timothy P Jenkins, Yasara Rathnayaka, Piyumali K Perera, Laura E Peachey, Matthew J Nolan, Lutz Krause, Rupika S Rajakaruna, Cinzia Cantacessi
Investigations of the impact that patent infections by soil-transmitted gastrointestinal nematode parasites exert on the composition of the host gut commensal flora are attracting growing interest by the scientific community. However, information collected to date varies across experiments, and further studies are needed to identify consistent relationships between parasites and commensal microbial species. Here, we explore the qualitative and quantitative differences between the microbial community profiles of cohorts of human volunteers from Sri Lanka with patent infection by one or more parasitic nematode species (H+), as well as that of uninfected subjects (H-) and of volunteers who had been subjected to regular prophylactic anthelmintic treatment (Ht)...
2017: PloS One
https://www.readbyqxmd.com/read/28889283/synthesis-of-32-p-c-di-gmp-for-diguanylate-cyclase-and-phosphodiesterase-activity-determinations
#8
Barbara I Kazmierczak
Diguanylate cyclases that synthesize and phosphodiesterases that hydrolyze the second messenger cyclic-di-GMP (c-di-GMP) are at the center of bacterial signaling pathways that control behaviors relevant to all aspects of microbial physiology and pathogenesis (Romling et al., Microbiol Mol Biol Rev 77(1):1-52, 2013). Bioinformatics tools can easily predict the presence of the diguanylate cyclase GGDEF domain, or the EAL and HD-GYP domains associated with phosphodiesterase activity. However, experimental confirmation of enzymatic activity is still necessary, as many proteins contain degenerate domains that lack catalytic activity but nonetheless function as c-di-GMP receptors...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28881972/abundance-estimation-and-differential-testing-on-strain-level-in-metagenomics-data
#9
Martina Fischer, Benjamin Strauch, Bernhard Y Renard
Motivation: Current metagenomics approaches allow analyzing the composition of microbial communities at high resolution. Important changes to the composition are known to even occur on strain level and to go hand in hand with changes in disease or ecological state. However, specific challenges arise for strain level analysis due to highly similar genome sequences present. Only a limited number of tools approach taxa abundance estimation beyond species level and there is a strong need for dedicated tools for strain resolution and differential abundance testing...
July 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28878086/metsv-a-novel-archaeal-lytic-virus-targeting-methanosarcina-strains
#10
Katrin Weidenbach, Lisa Nickel, Horst Neve, Omer S Alkhnbashi, Sven Künzel, Anne Kupczok, Thorsten Bauersachs, Liam Cassidy, Andreas Tholey, Rolf Backofen, Ruth A Schmitz
A novel archaeal lytic virus targeting species of the genus Methanosarcina was isolated using Methanosarcina mazei strain Gö1 as host. Due to its spherical morphology the virus was designated Methanosarcinaspherical virus (MetSV). Molecular analysis demonstrated that MetSV contains double stranded linear DNA with a genome size of 10,567 bp containing 22 open reading frames (ORFs) all oriented in the same direction. Functions were predicted for some of these ORFs, i. e. like DNA polymerase, ATPase, DNA-binding protein, as well as envelope (structural) protein...
September 6, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28869408/involvement-of-signal-peptidase-i-in-streptococcus-sanguinis-biofilm-formation
#11
Jessica Aynapudi, Fadi El-Rami, Xiuchun Ge, Victoria Stone, Bin Zhu, Todd Kitten, Ping Xu
Biofilm accounts for 65-80 % of microbial infections in humans. Considerable evidence links biofilm formation by oral microbiota to oral disease and consequently systemic infections. Streptococcus sanguinis, a Gram-positive bacterium, is one of the most abundant species of the oral microbiota and it contributes to biofilm development in the oral cavity. Due to its altered biofilm formation, we investigated a biofilm mutant, ΔSSA_0351, that is deficient in type I signal peptidase (SPase) in this study. Although the growth curve of the ΔSSA_0351 mutant showed no significant difference from that of the wild-type strain SK36, biofilm assays using both microtitre plate assay and confocal laser scanning microscopy (CLSM) confirmed a sharp reduction in biofilm formation in the mutant compared to the wild-type strain and the paralogous mutant ΔSSA_0849...
September 4, 2017: Microbiology
https://www.readbyqxmd.com/read/28861131/unique-down-to-our-microbes-assessment-of-an-inquiry-based-metagenomics-activity
#12
Thomas B Lentz, Laura E Ott, Sabrina D Robertson, Sarah C Windsor, Joshua B Kelley, Michael S Wollenberg, Robert R Dunn, Carlos C Goller
Metagenomics is an important method for studying microbial life. However, undergraduate exposure to metagenomics is hindered by associated software, computing demands, and dataset access. In this inquiry-based activity designed for introductory life science majors and nonmajors, students perform an investigation of the bacterial communities inhabiting the human belly button and associated metagenomics data collected through a citizen science project and visualized using an open-access bioinformatics tool. The activity is designed for attainment of the following student learning outcomes: defining terms associated with metagenomics analyses, describing the biological impact of the microbiota on human health, formulating a hypothesis, analyzing and interpreting metagenomics data to compare microbiota, evaluating a specific hypothesis, and synthesizing a conceptual model as to why bacterial populations vary...
2017: Journal of Microbiology & Biology Education: JMBE
https://www.readbyqxmd.com/read/28851370/comparing-microbiota-profiles-in-induced-and-spontaneous-sputum-samples-in-copd-patients
#13
Solveig Tangedal, Marianne Aanerud, Rune Grønseth, Christine Drengenes, Harald G Wiker, Per S Bakke, Tomas M Eagan
BACKGROUND: Induced and spontaneous sputum are used to evaluate the airways microbiota. Whether the sputum types can be used interchangeably in microbiota research is unknown. Our aim was to compare microbiota in induced and spontaneous sputum from COPD patients sampled during the same consultation. METHODS: COPD patients from Bergen, Norway, were followed between 2006/2010, examined during the stable state and exacerbations. 30 patients delivered 36 sample pairs...
August 29, 2017: Respiratory Research
https://www.readbyqxmd.com/read/28838410/the-microbiome-in-crohn-s-disease-role-in-pathogenesis-and-role-of-microbiome-replacement-therapies
#14
REVIEW
Sahil Khanna, Laura E Raffals
Individuals with a genetic predisposition to Crohn's disease develop aberrant immune responses to environmental triggers. The gastrointestinal microbiota is increasingly recognized to play an important role in the development of Crohn's disease. Decrease in global gut microbial diversity and specific bacterial alterations have been implicated in Crohn's disease. Advances in sequencing techniques and bioinformatics and correlation with host genetics continue to improve insight into the structure and function of the microbial community and interactions with the host immune system...
September 2017: Gastroenterology Clinics of North America
https://www.readbyqxmd.com/read/28837656/in-silico-analysis-of-protein-toxin-and-bacteriocins-from-lactobacillus-paracasei-sd1-genome-and-available-online-databases
#15
Komwit Surachat, Unitsa Sangket, Panchalika Deachamag, Wilaiwan Chotigeat
Lactobacillus paracasei SD1 is a potential probiotic strain due to its ability to survive several conditions in human dental cavities. To ascertain its safety for human use, we therefore performed a comprehensive bioinformatics analysis and characterization of the bacterial protein toxins produced by this strain. We report the complete genome of Lactobacillus paracasei SD1 and its comparison to other Lactobacillus genomes. Additionally, we identify and analyze its protein toxins and antimicrobial proteins using reliable online database resources and establish its phylogenetic relationship with other bacterial genomes...
2017: PloS One
https://www.readbyqxmd.com/read/28837129/large-scale-comparative-metagenomics-of-blastocystis-a-common-member-of-the-human-gut-microbiome
#16
Francesco Beghini, Edoardo Pasolli, Tin Duy Truong, Lorenza Putignani, Simone M Cacciò, Nicola Segata
The influence of unicellular eukaryotic microorganisms on human gut health and disease is still largely unexplored. Blastocystis spp. commonly colonize the gut, but its clinical significance and ecological role are currently unsettled. We have developed a high-sensitivity bioinformatic pipeline to detect Blastocystis subtypes (STs) from shotgun metagenomics, and applied it to 12 large data sets, comprising 1689 subjects of different geographic origin, disease status and lifestyle. We confirmed and extended previous observations on the high prevalence the microrganism in the population (14...
August 22, 2017: ISME Journal
https://www.readbyqxmd.com/read/28831186/the-ibd-interactome-an-integrated-view-of-aetiology-pathogenesis-and-therapy
#17
REVIEW
Heitor S P de Souza, Claudio Fiocchi, Dimitrios Iliopoulos
Crohn's disease and ulcerative colitis are prototypical complex diseases characterized by chronic and heterogeneous manifestations, induced by interacting environmental, genomic, microbial and immunological factors. These interactions result in an overwhelming complexity that cannot be tackled by studying the totality of each pathological component (an '-ome') in isolation without consideration of the interaction among all relevant -omes that yield an overall 'network effect'. The outcome of this effect is the 'IBD interactome', defined as a disease network in which dysregulation of individual -omes causes intestinal inflammation mediated by dysfunctional molecular modules...
August 23, 2017: Nature Reviews. Gastroenterology & Hepatology
https://www.readbyqxmd.com/read/28822547/bacterial-diversity-in-goat-milk-from-the-guanzhong-area-of-china
#18
Fuxin Zhang, Zhaoxia Wang, Feiyan Lei, Bini Wang, Shuaiming Jiang, Qiannan Peng, Jiachao Zhang, Yuyu Shao
In this study, the V3 and V4 regions of the 16S rRNA gene from metagenomic DNA were sequenced to identify differences in microbial diversity in raw milk of Saanen and Guanzhong goats from the Guanzhong area of China. The results showed that Proteobacteria was the predominant phylum, accounting for 71.31% of all phyla identified in milk from the 2 breeds, and Enterobacter was the predominant genus (24.69%) within the microbial community. Microbial alpha diversity from Saanen goat milk was significantly higher than that of Guanzhong goat milk based on bioinformatic analysis of indices of Chao1, Shannon, Simpson, observed species, and the abundance-based coverage estimator...
August 16, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28810907/schr%C3%A3-dinger-s-microbes-tools-for-distinguishing-the-living-from-the-dead-in-microbial-ecosystems
#19
REVIEW
Joanne B Emerson, Rachel I Adams, Clarisse M Betancourt Román, Brandon Brooks, David A Coil, Katherine Dahlhausen, Holly H Ganz, Erica M Hartmann, Tiffany Hsu, Nicholas B Justice, Ivan G Paulino-Lima, Julia C Luongo, Despoina S Lymperopoulou, Cinta Gomez-Silvan, Brooke Rothschild-Mancinelli, Melike Balk, Curtis Huttenhower, Andreas Nocker, Parag Vaishampayan, Lynn J Rothschild
While often obvious for macroscopic organisms, determining whether a microbe is dead or alive is fraught with complications. Fields such as microbial ecology, environmental health, and medical microbiology each determine how best to assess which members of the microbial community are alive, according to their respective scientific and/or regulatory needs. Many of these fields have gone from studying communities on a bulk level to the fine-scale resolution of microbial populations within consortia. For example, advances in nucleic acid sequencing technologies and downstream bioinformatic analyses have allowed for high-resolution insight into microbial community composition and metabolic potential, yet we know very little about whether such community DNA sequences represent viable microorganisms...
August 16, 2017: Microbiome
https://www.readbyqxmd.com/read/28807046/a-comprehensive-evaluation-of-the-sl1p-pipeline-for-16s-rrna-gene-sequencing-analysis
#20
Fiona J Whelan, Michael G Surette
BACKGROUND: Advances in next-generation sequencing technologies have allowed for detailed, molecular-based studies of microbial communities such as the human gut, soil, and ocean waters. Sequencing of the 16S rRNA gene, specific to prokaryotes, using universal PCR primers has become a common approach to studying the composition of these microbiota. However, the bioinformatic processing of the resulting millions of DNA sequences can be challenging, and a standardized protocol would aid in reproducible analyses...
August 14, 2017: Microbiome
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