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Microbial bioinformatics

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https://www.readbyqxmd.com/read/29340235/evidence-based-design-and-evaluation-of-a-whole-genome-sequencing-clinical-report-for-the-reference-microbiology-laboratory
#1
Anamaria Crisan, Geoffrey McKee, Tamara Munzner, Jennifer L Gardy
Background: Microbial genome sequencing is now being routinely used in many clinical and public health laboratories. Understanding how to report complex genomic test results to stakeholders who may have varying familiarity with genomics-including clinicians, laboratorians, epidemiologists, and researchers-is critical to the successful and sustainable implementation of this new technology; however, there are no evidence-based guidelines for designing such a report in the pathogen genomics domain...
2018: PeerJ
https://www.readbyqxmd.com/read/29335005/in-depth-resistome-analysis-by-targeted-metagenomics
#2
Val F Lanza, Fernando Baquero, José Luís Martínez, Ricardo Ramos-Ruíz, Bruno González-Zorn, Antoine Andremont, Antonio Sánchez-Valenzuela, Stanislav Dusko Ehrlich, Sean Kennedy, Etienne Ruppé, Willem van Schaik, Rob J Willems, Fernando de la Cruz, Teresa M Coque
BACKGROUND: Antimicrobial resistance is a major global health challenge. Metagenomics allows analyzing the presence and dynamics of "resistomes" (the ensemble of genes encoding antimicrobial resistance in a given microbiome) in disparate microbial ecosystems. However, the low sensitivity and specificity of available metagenomic methods preclude the detection of minority populations (often present below their detection threshold) and/or the identification of allelic variants that differ in the resulting phenotype...
January 15, 2018: Microbiome
https://www.readbyqxmd.com/read/29323384/tracking-iron-associated-proteomes-in-pathogens-by-a-fluorescence-approach
#3
Nan Jiang, Tianfan Cheng, Minji Wang, Godfrey Chi-Fung Chan, Lijian Jin, Hongyan Li, Hongzhe Sun
Porphyromonas gingivalis is a key oral anaerobic bacterium involved in human periodontitis, which may affect up to 15% adults worldwide. Using the membrane permeable fluorescent probe Fe-TRACER, we identified 17 iron-associated proteins in Porphyromonas gingivalis. We demonstrated the specific binding of the probe towards iron-associated proteins using transferrin as an example and provided an X-ray structure of the fluorescent probe-bound transferrin. Our study provides a basis for the understanding of iron homeostasis in pathogens, and our approach based on the integration of fluorescence imaging with proteomics and bioinformatics can be readily extended to mine other metalloproteomes in microbials...
January 11, 2018: Metallomics: Integrated Biometal Science
https://www.readbyqxmd.com/read/29322917/identification-of-natural-antimicrobial-peptides-from-bacteria-through-metagenomic-and-metatranscriptomic-analysis-of-high-throughput-transcriptome-data-of-taiwanese-oolong-teas
#4
Kai-Yao Huang, Tzu-Hao Chang, Jhih-Hua Jhong, Yu-Hsiang Chi, Wen-Chi Li, Chien-Lung Chan, K Robert Lai, Tzong-Yi Lee
BACKGROUND: Anti-microbial peptides (AMPs), naturally encoded by genes and generally containing 12-100 amino acids, are crucial components of the innate immune system and can protect the host from various pathogenic bacteria and viruses. In recent years, the widespread use of antibiotics has resulted in the rapid growth of antibiotic-resistant microorganisms that often induce critical infection and pathogenesis. Recently, the advent of high-throughput technologies has led molecular biology into a data surge in both the amount and scope of data...
December 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29318441/transforming-bacterial-disease-surveillance-and-investigation-using-whole-genome-sequence-to-probe-the-trace
#5
REVIEW
Biao Kan, Haijian Zhou, Pengcheng Du, Wen Zhang, Xin Lu, Tian Qin, Jianguo Xu
Two decades have passed since the first bacterial whole-genome sequencing, which provides new opportunity for microbial genome. Consequently, considerable genetic diversity encoded by bacterial genomes and among the strains in the same species has been revealed. In recent years, genome sequencing techniques and bioinformatics have developed rapidly, which has resulted in transformation and expedited the application of strategy and methodology for bacterial genome comparison used in dissection of infectious disease epidemics...
January 9, 2018: Frontiers of Medicine
https://www.readbyqxmd.com/read/29315344/culture-independent-analysis-of-liver-abscess-using-nanopore-sequencing
#6
Liang Gong, Yao-Ting Huang, Chee-Hong Wong, Wen-Cheng Chao, Zong-Yen Wu, Chia-Lin Wei, Po-Yu Liu
The identification of microbial species has depended predominantly upon culture-based techniques. However, the difficulty with which types of organisms are cultured implies that the grown species may be overrepresented by both cultivation and plate counts. In recent years, culture-independent analysis using high-throughput sequencing has been advocated for use as a point-of-care diagnostic tool. Although it offers a rapid and unbiased survey to characterize the pathogens in clinical specimens, its accuracy is reduced by the high level of contamination of human DNA...
2018: PloS One
https://www.readbyqxmd.com/read/29314766/gpsit-an-automated-method-for-evolutionary-analysis-of-nonculturable-ciliated-microeukaryotes
#7
Xiao Chen, Yurui Wang, Yalan Sheng, Alan Warren, Shan Gao
Microeukaryotes are among the most important components of the microbial food web in almost all aquatic and terrestrial ecosystems worldwide. In order to gain a better understanding their roles and functions in ecosystems, sequencing coupled with phylogenomic analyses of entire genomes or transcriptomes are increasingly used to reconstruct the evolutionary history and classification of these microeukaryotes and thus provide a more robust framework for determining their systematics and diversity. More importantly, phylogenomic research usually requires high levels of hands-on bioinformatics experience...
January 4, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29311639/exploring-viral-diversity-in-a-unique-south-african-soil-habitat
#8
Jane Segobola, Evelien Adriaenssens, Tsepo Tsekoa, Konanani Rashamuse, Don Cowan
The Kogelberg Biosphere Reserve in the Cape Floral Kingdom in South Africa is known for its unique plant biodiversity. The potential presence of unique microbial and viral biodiversity associated with this unique plant biodiversity led us to explore the fynbos soil using metaviromic techniques. In this study, metaviromes of a soil community from the Kogelberg Biosphere Reserve has been characterised in detail for the first time. Metaviromic DNA was recovered from soil and sequenced by Next Generation Sequencing...
January 8, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29309933/a-primer-on-microbial-bioinformatics-for-non-bioinformaticians
#9
REVIEW
J A Carriço, Mirko Rossi, Jacob Moran-Gilad, Gary Van Domselaar, Mário Ramirez
BACKGROUND: Presently, the bottleneck in the deployment of High Throughput Sequencing (HTS) technology is the ability to analyse the increasing amount of data produced in a fit-for-purpose manner. The field of Microbial Bioinformatics is thriving and quickly adapting to the technological changes, which creates difficulties for non-bioinformaticians to follow the complexity and increasing jargon of this field. AIMS: This review is directed towards non-bioinformaticians who wish to gain understanding of the overall microbial bioinformatic processes from the raw data obtained from the sequencers to the final outputs...
January 5, 2018: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/29290650/structural-shift-of-gut-microbiota-during-chemo-preventive-effects-of-epigallocatechin-gallate-on-colorectal-carcinogenesis-in-mice
#10
Xin Wang, Tao Ye, Wen-Jie Chen, You Lv, Zong Hao, Jun Chen, Jia-Ying Zhao, Hui-Peng Wang, Yuan-Kun Cai
AIM: To investigate the effect of epigallocatechin gallate (EGCG) on structural changes of gut microbiota in colorectal carcinogenesis. METHODS: An azoxymethane (AOM)/dextran sodium sulfate (DSS)-induced colitis mouse model was established. Forty-two female FVB/N mice were randomly divided into the following three groups: group 1 (10 mice, negative control) was treated with vehicle, group 2 (16 mice, positive control) was treated with AOM plus vehicle, and group 3 (16 mice, EG) was treated with AOM plus EGCG...
December 14, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/29287982/airway-microbial-metagenomics
#11
Katarzyna Pienkowska, Lutz Wiehlmann, Burkhard Tümmler
High-throughput untargeted metagenome sequencing provides information about the composition of the microbial communities of viruses, bacteria, archaea and unicellular eukaryotes in the habitat of interest. This review outlines the sampling, processing, sequencing and bioinformatic analysis of secretions of the respiratory tract and summarizes our current knowledge of the upper and lower human airways metagenome in health and disease.
December 26, 2017: Microbes and Infection
https://www.readbyqxmd.com/read/29281673/taxonomic-differences-of-gut-microbiomes-drive-cellulolytic-enzymatic-potential-within-hind-gut-fermenting-mammals
#12
Emma C L Finlayson-Trick, Landon J Getz, Patrick D Slaine, Mackenzie Thornbury, Emily Lamoureux, Jamie Cook, Morgan G I Langille, Lois E Murray, Craig McCormick, John R Rohde, Zhenyu Cheng
Host diet influences the diversity and metabolic activities of the gut microbiome. Previous studies have shown that the gut microbiome provides a wide array of enzymes that enable processing of diverse dietary components. Because the primary diet of the porcupine, Erethizon dorsatum, is lignified plant material, we reasoned that the porcupine microbiome would be replete with enzymes required to degrade lignocellulose. Here, we report on the bacterial composition in the porcupine microbiome using 16S rRNA sequencing and bioinformatics analysis...
2017: PloS One
https://www.readbyqxmd.com/read/29280312/dysbiosis-signatures-of-gut-microbiota-along-the-sequence-from-healthy-young-patients-to-those-with-overweight-and-obesity
#13
Renyuan Gao, Cuiling Zhu, Hao Li, Mingming Yin, Cheng Pan, Linsheng Huang, Cheng Kong, Xingchun Wang, Yi Zhang, Shen Qu, Huanlong Qin
OBJECTIVE: To investigate the gut microbiota in healthy volunteers (HVs), patients with overweight (OW), and patients with obesity (OB), including those with acanthosis nigricans (AN) or without AN (N-AN). METHODS: Microbial 16S rRNA genes were examined by using pyrosequencing technology and analyzed by using bioinformatics methods. RESULTS: Subjects in the OW and OB groups showed severe disturbances in glycemic control, lipid profile, and inflammatory markers (all P < 0...
December 27, 2017: Obesity
https://www.readbyqxmd.com/read/29274958/mining-metagenomic-and-metatranscriptomic-data-for-clues-about-microbial-metabolic-functions-in-ruminants
#14
Fuyong Li, Andre L A Neves, Bibaswan Ghoshal, Le Luo Guan
Metagenomics and metatranscriptomics can capture the whole genome and transcriptome repertoire of microorganisms through sequencing total DNA/RNA from various environmental samples, providing both taxonomic and functional information with high resolution. The unique and complex rumen microbial ecosystem is receiving great research attention because the rumen microbiota coevolves with the host and equips ruminants with the ability to convert cellulosic plant materials to high-protein products for human consumption...
December 20, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/29258574/micra-an-automatic-pipeline-for-fast-characterization-of-microbial-genomes-from-high-throughput-sequencing-data
#15
Ségolène Caboche, Gaël Even, Alexandre Loywick, Christophe Audebert, David Hot
The increase in available sequence data has advanced the field of microbiology; however, making sense of these data without bioinformatics skills is still problematic. We describe MICRA, an automatic pipeline, available as a web interface, for microbial identification and characterization through reads analysis. MICRA uses iterative mapping against reference genomes to identify genes and variations. Additional modules allow prediction of antibiotic susceptibility and resistance and comparing the results of several samples...
December 19, 2017: Genome Biology
https://www.readbyqxmd.com/read/29232712/bioinformatic-analysis-reveals-new-determinants-of-antigenic-14-3-3-proteins-and-a-novel-antifungal-strategy
#16
Jenna E McGowan, Jacqueline Kratch, Saurabh Chattopadhyay, Bina Joe, Heather R Conti, Ritu Chakravarti
The ubiquitously expressed 14-3-3 family of proteins is evolutionarily conserved from yeast to mammals. Their involvement in humoral and cellular immune responses is emerging through studies in drosophila and humans. In humans, a select group of 14-3-3 isoforms are antigenic; however the determinants of their antigenicity are not known. Here, we show that although mammalian 14-3-3 proteins are mostly conserved, subtle differences between their isoforms may give rise to their antigenicity. We observed syntenic relations among all the isoforms of 14-3-3 for mammals, but not with that of birds or amphibians...
2017: PloS One
https://www.readbyqxmd.com/read/29228191/frogs-find-rapidly-otus-with-galaxy-solution
#17
Frédéric Escudié, Lucas Auer, Maria Bernard, Mahendra Mariadassou, Laurent Cauquil, Katia Vidal, Sarah Maman, Guillermina Hernandez-Raquet, Sylvie Combes, Géraldine Pascal
Motivation: Metagenomics leads to major advances in microbial ecology and biologists need user friendly tools to analyze their data on their own. Results: This Galaxy-supported pipeline, called FROGS, is designed to analyze large sets of amplicon sequences and produce abundance tables of Operational Taxonomic Units (OTUs) and their taxonomic affiliation. The clustering uses Swarm. The chimera removal uses VSEARCH, combined with original cross-sample validation. The taxonomic affiliation returns an innovative multi-affiliation output to highlight databases conflicts and uncertainties...
December 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29212440/constax-a-tool-for-improved-taxonomic-resolution-of-environmental-fungal-its-sequences
#18
Kristi Gdanetz, Gian Maria Niccolò Benucci, Natalie Vande Pol, Gregory Bonito
BACKGROUND: One of the most crucial steps in high-throughput sequence-based microbiome studies is the taxonomic assignment of sequences belonging to operational taxonomic units (OTUs). Without taxonomic classification, functional and biological information of microbial communities cannot be inferred or interpreted. The internal transcribed spacer (ITS) region of the ribosomal DNA is the conventional marker region for fungal community studies. While bioinformatics pipelines that cluster reads into OTUs have received much attention in the literature, less attention has been given to the taxonomic classification of these sequences, upon which biological inference is dependent...
December 6, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29211828/asar-visual-analysis-of-metagenomes-in-r
#19
Askarbek Orakov, Nazgul Sakenova, Anatoly Sorokin, Igor Goryanin
Motivation: Functional and taxonomic analyses are critical steps in understanding interspecific interactions within microbial communities. Currently, such analyses are run separately, which complicates interpretation of results. Here we present the ASAR interactive tool for simultaneous analysis of metagenomic data in three dimensions: taxonomy, function, metagenome. Results: An interactive data analysis tool for selection, aggregation, and visualization of metagenomic data is presented...
December 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29208934/salmonella-small-rna-fragment-sal-1-facilitates-bacterial-survival-in-infected-cells-via-suppressing-inos-induction-in-a-microrna-manner
#20
Chihao Zhao, Zhen Zhou, Tianfu Zhang, Fenyong Liu, Chen-Yu Zhang, Ke Zen, Hongwei Gu
Salmonella can hijack host atypical miRNA processing machinery to cleave its small non-coding RNA into a ~22-nt RNA fragment, Sal-1, which facilitates Salmonella survival in the infected host. The mechanism through which Sal-1 promotes Salmonella survival, however, remains unknown. In the present study, we reported that Sal-1 targets cellular inducible nitric oxide synthase (iNOS) in a miRNA manner, leading to attenuation of host cell iNOS/NO-mediated anti-microbial capacity. First, depletion of Sal-1 in Salmonella-infected epithelial cells significantly increased the iNOS level but not the levels of various inflammatory cytokines...
December 5, 2017: Scientific Reports
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