keyword
MENU ▼
Read by QxMD icon Read
search

Microbial bioinformatics

keyword
https://www.readbyqxmd.com/read/29152584/large-scale-bioinformatics-analysis-of-bacillus-genomes-uncovers-conserved-roles-of-natural-products-in-bacterial-physiology
#1
Kirk J Grubbs, Rachel M Bleich, Kevin C Santa Maria, Scott E Allen, Sherif Farag, Elizabeth A Shank, Albert A Bowers
Bacteria possess an amazing capacity to synthesize a diverse range of structurally complex, bioactive natural products known as specialized (or secondary) metabolites. Many of these specialized metabolites are used as clinical therapeutics, while others have important ecological roles in microbial communities. The biosynthetic gene clusters (BGCs) that generate these metabolites can be identified in bacterial genome sequences using their highly conserved genetic features. We analyzed an unprecedented 1,566 bacterial genomes from Bacillus species and identified nearly 20,000 BGCs...
November 2017: MSystems
https://www.readbyqxmd.com/read/29150001/crispr-history-discovery-characterization-and-prosperity
#2
Wenyuan Han, Qunxin She
CRISPR research is a very young research field since it was only 10years ago when the system was found to confer antiviral defense. Nevertheless, there has been an explosion of publications in CRISPR research in the past 5years. The research was started with the comparative genomics of microbial genomes early this century, which revealed the prevalence of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) in bacteria and archaea. Series of hypotheses were made based on bioinformatics analyses and tested experimentally within a few years after the CRISPR acronym was coined...
2017: Progress in Molecular Biology and Translational Science
https://www.readbyqxmd.com/read/29134779/crochelins-siderophores-with-a-novel-iron-chelating-moiety-from-the-nitrogen-fixing-bacterium-azotobacter-chroococcum
#3
Oliver Baars, Xinning Zhang, Marcus I Gibson, Alan T Stone, Francois M M Morel, Mohammad R Seyedsayamdost
Microbes utilize siderophores to access essential iron resources. Over 500 siderophores are known, but they utilize a small set of common moieties to bind iron. Azotobacter chroococcum expresses iron-rich nitrogenases with which it reduces N2. Though an important agricultural inoculant, the structures of its iron-binding molecules remain unknown. Herein, we examine the 'chelome' of A. chroococcum using a small molecule discovery and bioinformatics approach. We find that it produces vibrioferrin and amphibactins as well as a novel family of siderophores, the crochelins...
November 14, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/29117585/metagenomics-profiling-for-assessing-microbial-diversity-in-both-active-and-closed-landfills
#4
Mohamad Yusof Zainun, Khanom Simarani
The municipal landfill is an example of human-made environment that harbours some complex diversity of microorganism communities. To evaluate this complexity, the structures of bacterial communities in active (operational) and closed (non-operational) landfills in Malaysia were analysed with culture independent metagenomics approaches. Several points of soil samples were collected from 0 to 20cm depth and were subjected to physicochemical test, such as temperature, pH, and moisture content. In addition, the heavy metal contamination was determined by using ICPMS...
November 5, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29116650/microbial-biotransformations-in-the-human-distal-gut
#5
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/29106667/microbiomedb-a-systems-biology-platform-for-integrating-mining-and-analyzing-microbiome-experiments
#6
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
#7
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/29104564/high-throughput-sequencing-for-detection-of-foodborne-pathogens
#8
REVIEW
Camilla Sekse, Arne Holst-Jensen, Ulrich Dobrindt, Gro S Johannessen, Weihua Li, Bjørn Spilsberg, Jianxin Shi
High-throughput sequencing (HTS) is becoming the state-of-the-art technology for typing of microbial isolates, especially in clinical samples. Yet, its application is still in its infancy for monitoring and outbreak investigations of foods. Here we review the published literature, covering not only bacterial but also viral and Eukaryote food pathogens, to assess the status and potential of HTS implementation to inform stakeholders, improve food safety and reduce outbreak impacts. The developments in sequencing technology and bioinformatics have outpaced the capacity to analyze and interpret the sequence data...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29098532/microbial-community-and-ovine-host-response-varies-with-early-and-late-stages-of-haemonchus-contortus-infection
#9
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/29096601/optimisation-of-16s-rrna-gut-microbiota-profiling-of-extremely-low-birth-weight-infants
#10
Cristina Alcon-Giner, Shabhonam Caim, Suparna Mitra, Jennifer Ketskemety, Udo Wegmann, John Wain, Gusztav Belteki, Paul Clarke, Lindsay J Hall
BACKGROUND: Infants born prematurely, particularly extremely low birth weight infants (ELBW) have altered gut microbial communities. Factors such as maternal health, gut immaturity, delivery mode, and antibiotic treatments are associated with microbiota disturbances, and are linked to an increased risk of certain diseases such as necrotising enterocolitis. Therefore, there is a requirement to optimally characterise microbial profiles in this at-risk cohort, via standardisation of methods, particularly for studying the influence of microbiota therapies (e...
November 2, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29092015/metacherchant-analyzing-genomic-context-of-antibiotic-resistance-genes-in-gut-microbiota
#11
Evgenii I Olekhnovich, Artem T Vasilyev, Vladimir I Ulyantsev, Elena S Kostryukova, Alexander V Tyakht
Motivation: Antibiotic resistance is an important global public health problem. Human gut microbiota is an accumulator of resistance genes potentially providing them to pathogens. It is important to develop tools for identifying the mechanisms of how resistance is transmitted between gut microbial species and pathogens. Results: We developed MetaCherchant - an algorithm for extracting the genomic environment of antibiotic resistance genes from metagenomic data in the form of a graph...
October 28, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29071712/the-role-of-the-microbiome-in-psoriasis-moving-from-disease-description-to-treatment-prediction
#12
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/29067467/analysis-of-microbial-community-composition-and-diversity-in-postoperative-intracranial-infection-using-high%C3%A2-throughput-sequencing
#13
Lixin Ruan, Daowu Wu, Xinchong Li, Qichuan Huang, Laipeng Lin, Jie Lin, Lie Chen, Peisong Xu, Jie Jin, Ningmin Yang, Xianfeng Li
Intracranial infection is one of the most serious complications following neurosurgery. It is well acknowledged that bacteria and fungi are the main pathogens responsible for postoperative intracranial infection. However, the microbial community structure, including composition, abundance and diversity, in postoperative intracranial infection is not fully understood, which greatly compromises our understanding of the necessity and effectiveness of postoperative antibiotic treatment. The present study collected eight cerebrospinal fluid (CSF) samples from patients with intracranial infection following neurosurgical procedures...
October 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29066778/structural-physicochemical-and-dynamic-features-conserved-within-the-aerolysin-pore-forming-toxin-family
#14
Nuria Cirauqui, Luciano A Abriata, F Gisou van der Goot, Matteo Dal Peraro
Aerolysin is the founding member of a major class of β-pore-forming toxins (β-PFTs) found throughout all kingdoms of life. PFTs are cytotoxic proteins produced as soluble monomers, which oligomerize at the membrane of target host cells forming pores that may lead to osmotic lysis and cell death. Besides their role in microbial infection, they have become interesting for their potential as biotechnological sensors and delivery systems. Using an approach that integrates bioinformatics with molecular modeling and simulation, we looked for conserved features across this large toxin family...
October 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29040493/releasing-the-geni-integrating-authentic-microbial-genomics-research-into-the-classroom-through-geni-act
#15
Karobi Moitra
The integration of genomics research into the undergraduate biology curriculum provides students with the opportunity to become familiar with bioinformatics tools and answer original research questions. Our purpose with this research project was to upscale the research experience through integration with classroom experience giving students access to authentic research projects. Students annotated 60 predicted ABC genes of Methanothermobacter thermautotrophicus and Methanobacterium sp. SWAN-1, and they were required to present a research poster to demonstrate their understanding of the project...
November 15, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/29039460/characterization-of-tree-shrew-tupaia-belangeri-interleukin-6-and-its-expression-pattern-in-response-to-exogenous-challenge
#16
Yuanyuan Han, Xiaomei Sun, Dexuan Kuang, Pinfen Tong, Caixia Lu, Wenguang Wang, Na Li, Yang Chen, Xiaoping Wang, Jiejie Dai, Huatang Zhang
Tree shrews, one of the closest relatives of primates, have attracted increasing attention as a model of human diseases, particularly for viral infections. As the first line of defense against microbial pathogens, the innate immune system is crucial in tree shrews. Interleukin-6 (IL-6) is important in the pathophysiology of infection, inflammation and cancer, where it promotes disease development or sustains immune reactions. The present study aimed to obtain further insight into the tree shrew IL-6 (tsIL-6) system, and the function of tsIL-6 in the antiviral and antibacterial response...
October 2, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/29036588/a-novel-data-structure-to-support-ultra-fast-taxonomic-classification-of-metagenomic-sequences-with-k-mer-signatures
#17
Xinan Liu, Ye Yu, Jinpeng Liu, Corrine F Elliott, Chen Qian, Jinze Liu
Motivation: Metagenomic read classification is a critical step in the identification and quantification of microbial species sampled by high-throughput sequencing. Although many algorithms have been developed to date, they suffer significant memory and/or computational costs. Due to the growing popularity of metagenomic data in both basic science and clinical applications, as well as the increasing volume of data being generated, efficient and accurate algorithms are in high demand. Results: We introduce MetaOthello, a probabilistic hashing classifier for metagenomic sequencing reads...
July 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036557/standardizing-biomass-reactions-and-ensuring-complete-mass-balance-in-genome-scale-metabolic-models
#18
Siu H J Chan, Jingyi Cai, Lin Wang, Margaret N Simons-Senftle, Costas D Maranas
Motivation: In a genome-scale metabolic model, the biomass produced is defined to have a molecular weight (MW) of 1 g mmol-1. This is critical for correctly predicting growth yields, contrasting multiple models and more importantly modeling microbial communities. However, the standard is rarely verified in the current practice and the chemical formulae of biomass components such as proteins, nucleic acids and lipids are often represented by undefined side groups (e.g. X, R). Results: We introduced a systematic procedure for checking the biomass weight and ensuring complete mass balance of a model...
November 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29026651/snvphyl-a-single-nucleotide-variant-phylogenomics-pipeline-for-microbial-genomic-epidemiology
#19
Aaron Petkau, Philip Mabon, Cameron Sieffert, Natalie C Knox, Jennifer Cabral, Mariam Iskander, Mark Iskander, Kelly Weedmark, Rahat Zaheer, Lee S Katz, Celine Nadon, Aleisha Reimer, Eduardo Taboada, Robert G Beiko, William Hsiao, Fiona Brinkman, Morag Graham, Gary Van Domselaar
The recent widespread application of whole-genome sequencing (WGS) for microbial disease investigations has spurred the development of new bioinformatics tools, including a notable proliferation of phylogenomics pipelines designed for infectious disease surveillance and outbreak investigation. Transitioning the use of WGS data out of the research laboratory and into the front lines of surveillance and outbreak response requires user-friendly, reproducible and scalable pipelines that have been well validated...
June 30, 2017: Microbial Genomics
https://www.readbyqxmd.com/read/29026445/viral-communities-of-the-human-gut-metagenomic-analysis-of-composition-and-dynamics
#20
REVIEW
Varun Aggarwala, Guanxiang Liang, Frederic D Bushman
BACKGROUND: The numerically most abundant biological entities on Earth are viruses. Vast populations prey on the cellular microbiota in all habitats, including the human gut. MAIN BODY: Here we review approaches for studying the human virome, and some recent results on movement of viral sequences between bacterial cells and eukaryotic hosts. We first overview biochemical and bioinformatic methods, emphasizing that specific choices in the methods used can have strong effects on the results obtained...
2017: Mobile DNA
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"