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Microbial bioinformatics

Huma Siddiqui, Tsute Chen, Ardita Aliko, Piotr M Mydel, Roland Jonsson, Ingar Olsen
BACKGROUND: Reduced salivation is considered a major clinical feature of most but not all cases of primary Sjögren's syndrome (pSS). Reduced saliva flow may lead to changes in the salivary microbiota. These changes have mainly been studied with culture that typically recovers only 65% of the bacteria present. OBJECTIVE: This study was to use high throughput sequencing, covering both cultivated and not-yet-cultivated bacteria, to assess the bacterial microbiota of whole saliva in pSS patients with normal salivation...
2016: Journal of Oral Microbiology
Seong-Tshool Hong
The human intestine contains a massive and complex microbial community called gut microbiota. A typical human carries 100 trillion microbes in his/her body which is 10 times greater than the number of their host cells, i.e. whole number of human cells. A combined microbial genome constituting gut microbiota is well excess our own human genome. The microbial composition of gut microbiotata and its role on diseases became a booming area of research, presenting a new paradigm of opportunities for modern medicines...
September 2016: Journal of Hypertension
María-Eugenia DeCastro, Esther Rodríguez-Belmonte, María-Isabel González-Siso
Microbial populations living in environments with temperatures above 50°C (thermophiles) have been widely studied, increasing our knowledge in the composition and function of these ecological communities. Since these populations express a broad number of heat-resistant enzymes (thermozymes), they also represent an important source for novel biocatalysts that can be potentially used in industrial processes. The integrated study of the whole-community DNA from an environment, known as metagenomics, coupled with the development of next generation sequencing (NGS) technologies, has allowed the generation of large amounts of data from thermophiles...
2016: Frontiers in Microbiology
Sundru Manjulata Devi, Subramanian Aishwarya, Prakash M Halami
The present study was aimed to evaluate the diversity and probiotic properties of Lactobacillus plantarum-group cultures from vegetable origin. First, genotypic diversity of L. plantarum (n=34) was achieved by PCR of Random Amplified Polymorphic DNA and recA gene-specific multiplex PCR. The isolates were segregated into five groups namely, Lactobacillus pentosus, Lactobacillus paraplantarum, Lactobacillus arizonensis, Lactobacillus plantarum subsp. plantarum and argentoratensis. Further discrimination was achieved by restriction fragment length polymorphism of probiotic adhesion genes viz...
October 5, 2016: Systematic and Applied Microbiology
Jiwoong Kim, Min Soo Kim, Andrew Y Koh, Yang Xie, Xiaowei Zhan
BACKGROUND: Given the lack of a complete and comprehensive library of microbial reference genomes, determining the functional profile of diverse microbial communities is challenging. The available functional analysis pipelines lack several key features: (i) an integrated alignment tool, (ii) operon-level analysis, and (iii) the ability to process large datasets. RESULTS: Here we introduce our open-sourced, stand-alone functional analysis pipeline for analyzing whole metagenomic and metatranscriptomic sequencing data, FMAP (Functional Mapping and Analysis Pipeline)...
October 10, 2016: BMC Bioinformatics
Lizi Bensoussan, Sarah Moraïs, Bareket Dassa, Nir Friedman, Bernard Henrissat, Vincent Lombard, Edward A Bayer, Itzhak Mizrahi
The cellulosome is an extracellular multi-enzyme complex that is considered one of the most efficient plant cell wall-degrading strategies devised by nature. Its unique modular architecture, achieved by high affinity and specific interaction between protein modules (cohesins and dockerins) enables formation of various enzyme combinations. Extensive research has been dedicated to the mechanistic nature of the cellulosome complex. Nevertheless, little is known regarding its distribution and abundance among microbes in natural plant fiber-rich environments...
October 6, 2016: Environmental Microbiology
Nengding Wang, Egon A Ozer
Transposon insertion sequencing is a process whereby microbial fitness determinants can be identified on a genome-wide scale. This process uses high-throughput next generation sequencing to screen for changes in the composition of a pool of transposon mutants after exposure to selective conditions. One commonly used process for generating transposon insertion sequencing libraries is called INSeq that works with mutant pools produced using a modified Mariner transposon. Libraries produced using the INSeq process are sequenced on the Illumina platform...
2017: Methods in Molecular Biology
Danielle S Kelley, Christopher W Lennon, Marlene Belfort, Olga Novikova
: Inteins are self-splicing protein elements that are mobile at the DNA level and are sporadically distributed across microbial genomes. Inteins appear to be horizontally transferred, and it has been speculated that phages may play a role in intein distribution. Our attention turns to mycobacteriophages, which infect mycobacteria, where both phage and host harbor inteins. Using bioinformatics, mycobacteriophage genomes were mined for inteins. This study reveals that these mobile elements are present across multiple mycobacteriophage clusters and are pervasive in certain genes, like the large terminase subunit TerL and a RecB-like nuclease, with the majority of intein-containing genes being phage specific...
October 4, 2016: MBio
Elisabeth M Bik
Recent developments in sequencing methods and bioinformatics analysis tools have greatly enabled the culture-independent analysis of complex microbial communities associated with environmental samples, plants, and animals. This has led to a spectacular increase in the number of studies on both membership and functionalities of these hitherto invisible worlds, in particular those of the human microbiome. The wide variety in available microbiome tools and platforms can be overwhelming, and making sound conclusions from scientific research can be challenging...
September 2016: Yale Journal of Biology and Medicine
Michael A Skinnider, Chad W Johnston, Robyn E Edgar, Chris A Dejong, Nishanth J Merwin, Philip N Rees, Nathan A Magarvey
Microbial natural products are an evolved resource of bioactive small molecules, which form the foundation of many modern therapeutic regimes. Ribosomally synthesized and posttranslationally modified peptides (RiPPs) represent a class of natural products which have attracted extensive interest for their diverse chemical structures and potent biological activities. Genome sequencing has revealed that the vast majority of genetically encoded natural products remain unknown. Many bioinformatic resources have therefore been developed to predict the chemical structures of natural products, particularly nonribosomal peptides and polyketides, from sequence data...
October 3, 2016: Proceedings of the National Academy of Sciences of the United States of America
Dragana Stanley, Linda J Mason, Kate E Mackin, Yogitha N Srikhanta, Dena Lyras, Monica D Prakash, Kulmira Nurgali, Andres Venegas, Michael D Hill, Robert J Moore, Connie H Y Wong
Bacterial infection is highly prevalent in patients who have had a stroke. Despite the potential contribution of micro-aspiration in post-stroke pneumonia, we found that the majority of the microorganisms detected in the patients who developed infections after having a stroke were common commensal bacteria that normally reside in the intestinal tracts. In a mouse model of ischemic stroke, post-stroke infection was only observed in mice that were born and raised in specific-pathogen-free facilities; this was not seen in mice that were born and raised in germ-free facilities...
October 3, 2016: Nature Medicine
Robert Häsler, Raheleh Sheibani-Tezerji, Anupam Sinha, Matthias Barann, Ateequr Rehman, Daniela Esser, Konrad Aden, Carolin Knecht, Berenice Brandt, Susanna Nikolaus, Sascha Schäuble, Christoph Kaleta, Andre Franke, Christoph Fretter, Werner Müller, Marc-Thorsten Hütt, Michael Krawczak, Stefan Schreiber, Philip Rosenstiel
OBJECTIVE: An inadequate host response to the intestinal microbiota likely contributes to the manifestation and progression of human inflammatory bowel disease (IBD). However, molecular approaches to unravelling the nature of the defective crosstalk and its consequences for intestinal metabolic and immunological networks are lacking. We assessed the mucosal transcript levels, splicing architecture and mucosa-attached microbial communities of patients with IBD to obtain a comprehensive view of the underlying, hitherto poorly characterised interactions, and how these are altered in IBD...
September 30, 2016: Gut
Samuel T Westreich, Ian Korf, David A Mills, Danielle G Lemay
BACKGROUND: Although metatranscriptomics-the study of diverse microbial population activity based on RNA-seq data-is rapidly growing in popularity, there are limited options for biologists to analyze this type of data. Current approaches for processing metatranscriptomes rely on restricted databases and a dedicated computing cluster, or metagenome-based approaches that have not been fully evaluated for processing metatranscriptomic datasets. We created a new bioinformatics pipeline, designed specifically for metatranscriptome dataset analysis, which runs in conjunction with Metagenome-RAST (MG-RAST) servers...
September 29, 2016: BMC Bioinformatics
Esther Singer, Bill Andreopoulos, Robert M Bowers, Janey Lee, Shweta Deshpande, Jennifer Chiniquy, Doina Ciobanu, Hans-Peter Klenk, Matthew Zane, Christopher Daum, Alicia Clum, Jan-Fang Cheng, Alex Copeland, Tanja Woyke
Generating sequence data of a defined community composed of organisms with complete reference genomes is indispensable for the benchmarking of new genome sequence analysis methods, including assembly and binning tools. Moreover the validation of new sequencing library protocols and platforms to assess critical components such as sequencing errors and biases relies on such datasets. We here report the next generation metagenomic sequence data of a defined mock community (Mock Bacteria ARchaea Community; MBARC-26), composed of 23 bacterial and 3 archaeal strains with finished genomes...
September 27, 2016: Scientific Data
Alessandro Tanca, Antonio Palomba, Cristina Fraumene, Daniela Pagnozzi, Valeria Manghina, Massimo Deligios, Thilo Muth, Erdmann Rapp, Lennart Martens, Maria Filippa Addis, Sergio Uzzau
BACKGROUND: Elucidating the role of gut microbiota in physiological and pathological processes has recently emerged as a key research aim in life sciences. In this respect, metaproteomics, the study of the whole protein complement of a microbial community, can provide a unique contribution by revealing which functions are actually being expressed by specific microbial taxa. However, its wide application to gut microbiota research has been hindered by challenges in data analysis, especially related to the choice of the proper sequence databases for protein identification...
September 27, 2016: Microbiome
Seong-Tshool Hong
The human intestine contains a massive and complex microbial community called gut microbiota. A typical human carries 100 trillion microbes in his/her body which is 10 times greater than the number of their host cells, i.e. whole number of human cells. A combined microbial genome constituting gut microbiota is well excess our own human genome. The microbial composition of gut microbiotata and its role on diseases became a booming area of research, presenting a new paradigm of opportunities for modern medicines...
September 2016: Journal of Hypertension
Minsuk Kim, Gwanggyu Sun, Dong-Yup Lee, Byung-Gee Kim
MOTIVATION: Modulation of regulatory circuits governing the metabolic processes is a crucial step for developing microbial cell factories. Despite the prevalence of in silico strain design algorithms, most of them are not capable of predicting required modifications in regulatory networks. Although a few algorithms may predict relevant targets for transcriptional regulator (TR) manipulations, they have limited reliability and applicability due to their high dependency on the availability of integrated metabolic/regulatory models...
September 7, 2016: Bioinformatics
Javier F Tabima, Sydney E Everhart, Meredith M Larsen, Alexandra J Weisberg, Zhian N Kamvar, Matthew A Tancos, Christine D Smart, Jeff H Chang, Niklaus J Grünwald
Development of tools to identify species, genotypes, or novel strains of invasive organisms is critical for monitoring emergence and implementing rapid response measures. Molecular markers, although critical to identifying species or genotypes, require bioinformatic tools for analysis. However, user-friendly analytical tools for fast identification are not readily available. To address this need, we created a web-based set of applications called Microbe-ID that allow for customizing a toolbox for rapid species identification and strain genotyping using any genetic markers of choice...
2016: PeerJ
Gregory J S Fowler, Ana G Pereira-Medrano, Stephen Jaffe, Grzegorz Pasternak, Trong Khoa Pham, Pablo Ledezma, Simon T E Hall, Ioannis A Ieropoulos, Phillip C Wright
Anodophilic bacteria have the ability to generate electricity in microbial fuel cells (MFCs) by extracellular electron transfer to the anode. We investigated the anode-specific responses of Shewanella oneidensis MR-1, an exoelectroactive Gammaproteobacterium, using for the first time iTRAQ and 2D-LC MS/MS driven membrane proteomics to compare protein abundances in S. oneidensis when generating power in MFCs, and growing in a continuous culture. The regulated dataset produced was enriched in membrane proteins...
September 7, 2016: Proteomics
Samuele Girotto, Cinzia Pizzi, Matteo Comin
MOTIVATION: Sequencing technologies allow the sequencing of microbial communities directly from the environment without prior culturing. Taxonomic analysis of microbial communities, a process referred to as binning, is one of the most challenging tasks when analyzing metagenomic reads data. The major problems are the lack of taxonomically related genomes in existing reference databases, the uneven abundance ratio of species and the limitations due to short read lengths and sequencing errors...
September 1, 2016: Bioinformatics
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