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Microbial bioinformatics

Kassi L Kosnicki, Jerrold C Penprase, Patricia Cintora, Pedro J Torres, Greg L Harris, Susan M Brasser, Scott T Kelley
Many alcohol-induced health complications are directly attributable to the toxicity of alcohol or its metabolites, but another potential health impact of alcohol may be on the microbial communities of the human gut. Clear distinctions between healthy and diseased-state gut microbiota have been observed in subjects with metabolic diseases, and recent studies suggest that chronic alcoholism is linked to gut microbiome dysbiosis. Here, we investigated the effects of moderate levels of alcohol consumption on the gut microbiome in both rats and humans...
May 11, 2018: Addiction Biology
Jialu Hu, Yiqun Gao, Yan Zheng, Xuequn Shang
BACKGROUND: The human body is colonized by a vast number of microbes. Microbiota can benefit many normal life processes, but can also cause many diseases by interfering the regular metabolism and immune system. Recent studies have demonstrated that the microbial community is closely associated with various types of cell carcinoma. The search for key factors, which also refer to cancer causing agents, can provide an important clue in understanding the regulatory mechanism of microbiota in uterine cervix cancer...
April 24, 2018: BMC Systems Biology
Arianna Tocchetti, Stefano Donadio, Margherita Sosio
The exponential increase in available microbial genome sequences coupled with predictive bioinformatic tools is underscoring the genetic capacity of bacteria to produce an unexpected large number of specialized bioactive compounds. Since most of the biosynthetic gene clusters (BGCs) present in microbial genomes are cryptic, i.e. not expressed under laboratory conditions, a variety of cloning systems and vectors have been devised to harbor DNA fragments large enough to carry entire BGCs and to allow their transfer in suitable heterologous hosts...
May 1, 2018: FEMS Microbiology Letters
Alex Sander Rodrigues Cangussu, Deborah Aires Almeida, Raimundo Wagner de Souza Aguiar, Sidnei Emilio Bordignon-Junior, Kelvinson Fernandes Viana, Luiz Carlos Bertucci Barbosa, Edson Wagner da Silva Cangussu, Igor Viana Brandi, Augustus Caeser Franke Portella, Gil Rodrigues Dos Santos, Eliane Macedo Sobrinho, William James Nogueira Lima
Phytase plays a prominent role in monogastric animal nutrition due to its ability to improve phytic acid digestion in the gastrointestinal tract, releasing phosphorus and other micronutrients that are important for animal development. Moreover, phytase decreases the amounts of phytic acid and phosphate excreted in feces. Bioinformatics approaches can contribute to the understanding of the catalytic structure of phytase. Analysis of the catalytic structure can reveal enzymatic stability and the polarization and hydrophobicity of amino acids...
2018: Enzyme Research
Chao Du, Gilles P van Wezel
Natural products (NPs) are a major source of compounds for the medical, agricultural and biotechnological industry. Many of these compounds are of microbial origin, and in particular from Actinobacteria or filamentous fungi. To successfully identify novel compounds that correlate to a bioactivity of interest, or discover new enzymes with desired functions, systematic multi-omics approaches have been developed over the years. Bioinformatics tools harness the rapidly expanding wealth of genome sequence information, revealing previously unsuspected biosynthetic diversity...
April 30, 2018: Proteomics
Blair Lawley, Manuela Centanni, Jun Watanabe, Ian Sims, Susan Carnachan, Roland Broadbent, Pheng Soon Lee, Khai Hong Wong, Gerald W Tannock
Members of the bacterial genus Bifidobacterium generally dominate the faecal microbiota of infants. The species B. longum is prevalent, but the subspecies longum and infantis that are known to colonize the infant bowel are not usually differentiated in microbiota investigations. These subspecies differ in their capacity to metabolize Human Milk Oligosaccharides (HMO) and may have differing ecological and symbiotic roles in humans. Quantitative PCR provides a quick analytical method by which to accurately ascertain the abundances of target species in microbiotas and microcosms...
April 27, 2018: Applied and Environmental Microbiology
Tammy C Tobin, Ashley Shade
Microbiology increasingly relies upon bioinformatics to understand complex microbial interactions. Nevertheless, biology undergraduates often lack the basic quantitative and computer-based skills required for bioinformatics analyses. To address these issues, the course module 'A Town on Fire! 16S rRNA Gene Amplicon Analysis of Microbial Communities Overlying the Centralia, PA Mine Fire' was developed for an undergraduate microbiology lecture course. In this module, microbiology students used Quantitative Insights into Microbial Ecology (QIIME) to perform taxonomic, phylogenetic and statistical analyses on bacterial communities from three hot mine fire-impacted surface soils using 16S rRNA gene amplicon sequences...
April 23, 2018: FEMS Microbiology Letters
Chase M Clark, Maria S Costa, Laura M Sanchez, Brian T Murphy
For decades, researchers have lacked the ability to rapidly correlate microbial identity with bacterial metabolism. Since specialized metabolites are critical to bacterial function and survival in the environment, we designed a data acquisition and bioinformatics technique (IDBac) that utilizes in situ matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to analyze protein and specialized metabolite spectra recorded from single bacterial colonies picked from agar plates...
April 23, 2018: Proceedings of the National Academy of Sciences of the United States of America
T A McAllister, L Dunière, P Drouin, S Xu, Y Wang, K Munns, R Zaheer
Ensiling of forages was recognized as a microbial-driven process as early as the late 1800s, when it was associated with the production of "sweet" or "sour" silage. Classical microbiological plating techniques defined the epiphytic microbial populations associated with fresh forage, the pivotal role of lactic acid-producing bacteria in the ensiling process, and the contribution of clostridia, bacilli, yeast, and molds to the spoilage of silage. Many of these classical studies focused on the enumeration and characterization of a limited number of microbial species that could be readily isolated on selective media...
May 2018: Journal of Dairy Science
Lydia K Greene, Erin A McKenney
OBJECTIVES: The aye-aye (Daubentonia madagascariensis) is famous for its feeding strategies that target structurally defended, but high-quality resources. Nonetheless, the influence of this digestible diet on gut microbial contributions to aye-aye metabolism and nutrition remains unexplored. When four captive aye-ayes were unexpectedly lost to persin toxicity, we opportunistically collected samples along the animals' gastrointestinal tracts. Here we describe the diversity and composition of appendicular, cecal, and colonic consortia relative to the aye-aye's unusual feeding ecology...
April 17, 2018: American Journal of Physical Anthropology
Rhitu Kotoky, Jina Rajkumari, Piyush Pandey
Microbial communities are an essential part of plant rhizosphere and participate in the functioning of plants, including rhizoremediation of petroleum contaminants. Rhizoremediation is a promising technology for removal of polyaromatic hydrocarbons based on interactions between plants and microbiome in the rhizosphere. Root exudation in the rhizosphere provides better nutrient uptake for rhizosphere microbiome, and therefore it is considered to be one of the major factors of microbial community function in the rhizosphere that plays a key role in the enhanced PAH biodegradation...
April 13, 2018: Journal of Environmental Management
Timothy Dallman, Philip Ashton, Ulf Schafer, Aleksey Jironkin, Anais Painset, Sharif Shaaban, Hassan Hartman, Richard Myers, Anthony Underwood, Claire Jenkins, Kathie Grant
Summary: We announce the release of SnapperDB v1.0 a program for scalable routine SNP analysis and storage of microbial populations. Availability: SnapperDB is implemented as a python application under the open source BSD license. All code and user guides are available at Reference genomes and SnapperDB configs are available at Contact: tim...
April 5, 2018: Bioinformatics
Luis M Rodriguez-R, Santosh Gunturu, James M Tiedje, James R Cole, Konstantinos T Konstantinidis
Estimations of microbial community diversity based on metagenomic data sets are affected, often to an unknown degree, by biases derived from insufficient coverage and reference database-dependent estimations of diversity. For instance, the completeness of reference databases cannot be generally estimated since it depends on the extant diversity sampled to date, which, with the exception of a few habitats such as the human gut, remains severely undersampled. Further, estimation of the degree of coverage of a microbial community by a metagenomic data set is prohibitively time-consuming for large data sets, and coverage values may not be directly comparable between data sets obtained with different sequencing technologies...
May 2018: MSystems
Dharmela Sellvam, Nyok Sean Lau, Yahya Mat Arip
Malaysia is one of the countries that are loaded with mega biodiversity which includes microbial communities. Phages constitute the major component in the microbial communities and yet the numbers of discovered phages are just a minute fraction of its population in the biosphere. Taking into account of a huge numbers of waiting to be discovered phages, a new bacteriophage designated as Escherichia phage YD-2008.s was successfully isolated using Escherichia coli ATCC 11303 as the host. Phage YD-2008.s poses icosahedral head measured at 57nm in diameter with a long non-contractile flexible tail measured at 107nm; proving the phage as one of the members of Siphoviridae family under the order of Caudovirales ...
March 2018: Tropical Life Sciences Research
S W Zhu, Z J Liu, M Li, H Q Zhu, L P Duan
OBJECTIVE: To assess whether the same biological conclusion, diagnostic or curative effects regarding microbial composition of irritable bowel syndrome (IBS) patients could be reached through different bioinformatics pipelines, we used two common bioinformatics pipelines (Uparse V2.0 and Mothur V1.39.5)to analyze the same fecal microbial 16S rRNA high-throughput sequencing data. METHODS: The two pipelines were used to analyze the diversity and richness of fecal microbial 16S rRNA high-throughput sequencing data of 27 samples, including 9 healthy controls (HC group), 9 diarrhea IBS patients before (IBS group) and after Rifaximin treatment (IBS-treatment, IBSt group)...
April 18, 2018: Beijing da Xue Xue Bao. Yi Xue Ban, Journal of Peking University. Health Sciences
Jonathan Mercier, Adrien Josso, Claudine Médigue, David Vallenet
BACKGROUND: High quality functional annotation is essential for understanding the phenotypic consequences encoded in a genome. Despite improvements in bioinformatics methods, millions of sequences in databanks are not assigned reliable functions. The curation of protein functions in the context of biological processes is a way to evaluate and improve their annotation. RESULTS: We developed an expert system using paraconsistent logic, named GROOLS (Genomic Rule Object-Oriented Logic System), that evaluates the completeness and the consistency of predicted functions through biological processes like metabolic pathways...
April 11, 2018: BMC Bioinformatics
Morgan G I Langille
Microbiome studies typically focus on characterizing the taxonomic and functional profiles of the microbes within a community. Functional profiling is generally thought to be superior to taxonomic profiling for investigating human-microbe interactions, but there are several limitations and challenges to existing approaches. This Perspective discusses the current sequencing and bioinformatic methods for producing taxonomic and functional profiles, recent studies utilizing and comparing these technologies, and the existing challenges and limitations of these data...
March 2018: MSystems
George Liechti, Raghuveer Singh, Patricia L Rossi, Miranda D Gray, Nancy E Adams, Anthony T Maurelli
Peptidoglycan is a sugar/amino acid polymer unique to bacteria and essential for division and cell shape maintenance. The d-amino acids that make up its cross-linked stem peptides are not abundant in nature and must be synthesized by bacteria de novo d-Glutamate is present at the second position of the pentapeptide stem and is strictly conserved in all bacterial species. In Gram-negative bacteria, d-glutamate is generated via the racemization of l-glutamate by glutamate racemase (MurI). Chlamydia trachomatis is the leading cause of infectious blindness and sexually transmitted bacterial infections worldwide...
April 3, 2018: MBio
Caroline Keegan, Stephan Krutzik, Mirjam Schenk, Philip O Scumpia, Jing Lu, Yan Ling Joy Pang, Brandon S Russell, Kok Seong Lim, Scarlet Shell, Erin Prestwich, Dan Su, David Elashoff, Robert M Hershberg, Barry R Bloom, John T Belisle, Sarah Fortune, Peter C Dedon, Matteo Pellegrini, Robert L Modlin
Upon recognition of a microbial pathogen, the innate and adaptive immune systems are linked to generate a cell-mediated immune response against the foreign invader. The culture filtrate of Mycobacterium tuberculosis contains ligands, such as M. tuberculosis tRNA, that activate the innate immune response and secreted Ags recognized by T cells to drive adaptive immune responses. In this study, bioinformatics analysis of gene-expression profiles derived from human PBMCs treated with distinct microbial ligands identified a mycobacterial tRNA-induced innate immune network resulting in the robust production of IL-12p70, a cytokine required to instruct an adaptive Th1 response for host defense against intracellular bacteria...
April 2, 2018: Journal of Immunology: Official Journal of the American Association of Immunologists
Carolyn A Brotherton, Marnix H Medema, E Peter Greenberg
Microbes are a major source of antibiotics, pharmaceuticals, and other bioactive compounds. The production of many specialized microbial metabolites is encoded in biosynthetic gene clusters (BGCs). A challenge associated with natural product discovery is that many BGCs are not expressed under laboratory growth conditions. Here we report a genome-mining approach to discover BGCs with luxR -type quorum sensing (QS) genes, which code for regulatory proteins that control gene expression. Our results show that BGCs linked to genes coding for LuxR-like proteins are widespread in Proteobacteria ...
May 2018: MSystems
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