keyword
MENU ▼
Read by QxMD icon Read
search

Microbial bioinformatics

keyword
https://www.readbyqxmd.com/read/28637301/eden-evolutionary-dynamics-within-environments
#1
Philipp C Münch, Bärbel Stecher, Alice C McHardy
Summary: Metagenomics revolutionized the field of microbial ecology, giving access to Gb-sized datasets of microbial communities under natural conditions. This enables fine-grained analyses of the functions of community members, studies of their association with phenotypes and environments, as well as of their microevolution and adaptation to changing environmental conditions. However, phylogenetic methods for studying adaptation and evolutionary dynamics are not able to cope with big data...
June 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28632895/genome-mining-reveals-high-incidence-of-putative-lipopeptide-biosynthesis-nrps-pks-clusters-containing-fatty-acyl-amp-ligase-genes-in-biofilm-forming-cyanobacteria
#2
Tomáš Galica, Pavel Hrouzek, Jan Mareš
Cyanobacterial lipopeptides exhibit antimicrobial and antifungal bioactivities with potential for use in pharmaceutical research. However, due to their haemolytic activity and cytotoxic effects against human cells, they may pose a health issue if produced in substantial amounts in the environment. In bacteria, lipopeptides can be synthesized via several well-evidenced mechanisms. In one of them, fatty acyl-AMP ligase (FAAL) initiates the biosynthesis by activation of a fatty acyl residue. We have performed a bioinformatic survey of the cyanobacterial genomic information available in the public databases for the presence of FAAL-containing non-ribosomal peptide synthetase/polyketide synthetase (NRPS/PKS) biosynthetic clusters, as a genetic basis for lipopeptide biosynthesis...
June 20, 2017: Journal of Phycology
https://www.readbyqxmd.com/read/28625995/novel-antibiotic-resistance-determinants-from-agricultural-soil-exposed-to-antibiotics-widely-used-in-human-medicine-and-animal-farming
#3
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/28625914/prioritizing-disease-causing-microbes-based-on-random-walking-on-the-heterogeneous-network
#4
Xianjun Shen, Yao Chen, Xingpeng Jiang, Xiaohua Hu, Tingting He, Jincai Yang
As we all know, the microbiota show remarkable variability within individuals. At the same time, those microorganisms living in the human body play a very important role in our health and disease, so the identification of the relationships between microbes and diseases will contribute to better understanding of microbes interactions, mechanism of functions. However, the microbial data which are obtained through the related technical sequencing is too much, but the known associations between the diseases and microbes are very less...
June 15, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28609785/comprehensive-analysis-of-microorganisms-accompanying-human-archaeological-remains
#5
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/28605849/a-next-generation-sequencing-approach-with-a-suitable-bioinformatics-workflow-to-study-fungal-diversity-in-bioaerosols-released-from-two-different-types-of-composting-plants
#6
Hamza Mbareche, Marc Veillette, Laetitia Bonifait, Marie-Eve Dubuis, Yves Benard, Geneviève Marchand, Guillaume J Bilodeau, Caroline Duchaine
Composting is used all over the world to transform different types of organic matter through the actions of complex microbial communities. Moving and handling composting material may lead to the emission of high concentrations of bioaerosols. High exposure levels are associated with adverse health effects among compost industry workers. Fungal spores are suspected to play a role in many respiratory illnesses. There is a paucity of information related to the detailed fungal diversity in compost as well as in the aerosols emitted through composting activities...
June 7, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28591840/novel-approaches-in-function-driven-single-cell-genomics
#7
Devin F R Doud, Tanja Woyke
Deeper sequencing and improved bioinformatics in conjunction with single-cell and metagenomic approaches continue to illuminate undercharacterized environmental microbial communities. This has propelled the 'who is there, and what might they be doing' paradigm to the uncultivated and has already radically changed the topology of the tree of life and provided key insights into the microbial contribution to biogeochemistry. While characterization of 'who' based on marker genes can describe a large fraction of the community, answering 'what are they doing' remains the elusive pinnacle for microbiology...
June 7, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28588568/food-safety-in-the-age-of-next-generation-sequencing-bioinformatics-and-open-data-access
#8
REVIEW
Eduardo N Taboada, Morag R Graham, João A Carriço, Gary Van Domselaar
Public health labs and food regulatory agencies globally are embracing whole genome sequencing (WGS) as a revolutionary new method that is positioned to replace numerous existing diagnostic and microbial typing technologies with a single new target: the microbial draft genome. The ability to cheaply generate large amounts of microbial genome sequence data, combined with emerging policies of food regulatory and public health institutions making their microbial sequences increasingly available and public, has served to open up the field to the general scientific community...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28584447/analysis-of-eawag-bbd-pathway-prediction-system-for-the-identification-of-malathion-degrading-microbes
#9
Subramaniam Sivakumar, Palanivel Anitha, Balsubramanian Ramesh, Gopal Suresh
Insecticides are the toxic substances that are used to kill insects. The use of insecticides is believed to be one of the major factors behind the increase in agricultural productivity in the 20th century. The organophosphates are now the largest and most versatile class of insecticide used and Malathion is the predominant type utilized. The accumulation of Malathion in environment is the biggest threat to the environment because of its toxicity. Malathion is lethal to beneficial insects, snails, micro crustaceans, fish, birds, amphibians, and soil microorganisms...
2017: Bioinformation
https://www.readbyqxmd.com/read/28574575/genomics-of-antibiotic-resistance-prediction-in-pseudomonas-aeruginosa
#10
REVIEW
Julie Jeukens, Luca Freschi, Irena Kukavica-Ibrulj, Jean-Guillaume Emond-Rheault, Nicholas P Tucker, Roger C Levesque
Antibiotic resistance is a worldwide health issue spreading quickly among human and animal pathogens, as well as environmental bacteria. Misuse of antibiotics has an impact on the selection of resistant bacteria, thus contributing to an increase in the occurrence of resistant genotypes that emerge via spontaneous mutation or are acquired by horizontal gene transfer. There is a specific and urgent need not only to detect antimicrobial resistance but also to predict antibiotic resistance in silico. We now have the capability to sequence hundreds of bacterial genomes per week, including assembly and annotation...
June 2, 2017: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/28569339/high-resolution-melting-as-a-rapid-reliable-accurate-and-cost-effective-emerging-tool-for-genotyping-pathogenic-bacteria-and-enhancing-molecular-epidemiological-surveillance-a-comprehensive-review-of-the-literature
#11
M Tamburro, G Ripabelli
INTRODUCTION: Rapid, reliable and accurate molecular typing methods are essential for outbreaks detection and infectious diseases control, for monitoring the evolution and dynamics of microbial populations, and for effective epidemiological surveillance. The introduction of a novel method based on the analysis of melting temperature of amplified products, known as High Resolution Melting (HRM) since 2002, has found applications in epidemiological studies, either for identification of bacterial species or molecular typing, as well as an extensive and increasing use in many research fields...
July 2017: Annali di Igiene: Medicina Preventiva e di Comunità
https://www.readbyqxmd.com/read/28560604/anthropogenic-protection-alters-the-microbiome-in-intertidal-mangrove-wetlands-in-hainan-island
#12
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/28559161/dna-metabarcoding-to-assess-indoor-fungal-communities-electrostatic-dust-collectors-and-illumina-sequencing
#13
Steffi Rocchi, Benoit Valot, Gabriel Reboux, Laurence Millon
DNA metabarcoding is increasingly being used to characterize the microbiological composition of both the indoor and outdoor environments of dwellings. Our study aimed to evaluate metabarcoding and bioinformatic analysis resulting from calibrated samples and samples collected by an electrostatic dust collector (EDC) in dwellings with no moisture problems. Thus, the fungal communities of 14 dwellings (eastern France, Franche-Comté region) were analyzed by Illumina MiSeq technology after amplification of the ITS2 region...
May 27, 2017: Journal of Microbiological Methods
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
#14
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/28533216/a-diverse-community-to-study-communities-integration-of-experiments-and-mathematical-models-to-study-microbial-consortia
#15
Antonella Succurro, Fiona Wanjiku Moejes, Oliver Ebenhöh
The last few years have seen the advancement of high-throughput experimental techniques produce an extraordinary amount of data. Bioinformatics and statistical analyses have become instrumental to interpreting the information coming from e.g. sequencing data, and often motivate further targeted experiments. The broad discipline of "computational biology" spans far beyond the well-established field of bioinformatics, but it is our impression that more theoretical methods like mathematical models are not yet as well integrated in the research studying microbial interactions...
May 22, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28509357/characterization-of-microbial-mixtures-by-mass-spectrometry
#16
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
#17
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/28498899/magenta-a-galaxy-implemented-tool-for-complete-tn-seq-analysis-and-data-visualization
#18
Katherine Maia McCoy, Margaret L Antonio, Tim van Opijnen
Motivation: Transposon insertion sequencing (Tn-Seq) is a microbial systems-level tool, that can determine on a genome-wide scale and in high-throughput, whether a gene, or a specific genomic region, is important for fitness under a specific experimental condition. Results: Here, we present MAGenTA, a suite of analysis tools which accurately calculate the growth rate for each disrupted gene in the genome to enable the discovery of: a) new leads for gene function, b) non coding RNAs; c) genes, pathways and ncRNAs that are involved in tolerating drugs or induce disease; d) higher order genome organization; and e) host-factors that affect bacterial host susceptibility...
May 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28494549/-changes-in-the-composition-of-intestinal-microbiota-in-mice-with-acute-liver-failure-induced-by-d-galactosamine
#19
Y X Hu, L Yu, H J Liu, M L Cheng
Objective: To investigate the changes in the composition of intestinal microbiota in mice with acute liver failure and identify characteristic bacteria, and to provide a basis for the diagnosis and treatment of acute liver failure with intestinal microbiota disorders. Methods: A total of 30 specific pathogen-free male BALB/c mice were used in this study, including 25 mice in the model group and 5 mice in the control group. An acute liver failure model was induced by D-galactosamine. Microbial DNA was extracted from intestinal contents in different segments of the lower digestive tract (ileum and colon) and feces and then were amplified using PCR...
April 20, 2017: Zhonghua Gan Zang Bing za Zhi, Zhonghua Ganzangbing Zazhi, Chinese Journal of Hepatology
https://www.readbyqxmd.com/read/28487430/rna-dependent-cysteine-biosynthesis-in-bacteria-and-archaea
#20
Takahito Mukai, Ana Crnković, Takuya Umehara, Natalia N Ivanova, Nikos C Kyrpides, Dieter Söll
The diversity of the genetic code systems used by microbes on earth is yet to be elucidated. It is known that certain methanogenic archaea employ an alternative system for cysteine (Cys) biosynthesis and encoding; tRNA(Cys) is first acylated with phosphoserine (Sep) by O-phosphoseryl-tRNA synthetase (SepRS) and then converted to Cys-tRNA(Cys) by Sep-tRNA:Cys-tRNA synthase (SepCysS). In this study, we searched all genomic and metagenomic protein sequence data in the Integrated Microbial Genomes (IMG) system and at the NCBI to reveal new clades of SepRS and SepCysS proteins belonging to diverse archaea in the four major groups (DPANN, Euryarchaeota, TACK, and Asgard) and two groups of bacteria ("Candidatus Parcubacteria" and Chloroflexi)...
May 9, 2017: MBio
keyword
keyword
4966
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"