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[PMID]: 28453677 [Au] Autor: Liu Y; Ripp F; Koeppel R; Schmidt H; Hellmann SL; Weber M; Krombholz CF; Schmidt B; Hankeln T [Ad] Endereço: Institute of Computer Science, Johannes Gutenberg University Mainz, 55099 Mainz, Germany. [Ti] Título: AFS: identification and quantification of species composition by metagenomic sequencing. [So] Source: Bioinformatics;33(9):1396-1398, 2017 May 01. [Is] ISSN: 1367-4811 [Cp] País de publicação: England [La] Idioma: eng [Ab] Resumo: Summary: DNA-based methods to detect and quantify taxon composition in biological materials are often based on species-specific polymerase chain reaction, limited to detecting species targeted by the assay. Next-generation sequencing overcomes this drawback by untargeted shotgun sequencing of whole metagenomes at affordable cost. Here we present AFS, a software pipeline for quantification of species composition in food. AFS uses metagenomic shotgun sequencing and sequence read counting to infer species proportions. Using Illumina data from a reference sausage comprising four species, we reveal that AFS is independent of the sequencing assay and library preparation protocol. Cost-saving short (50-bp) single-end reads and Nextera ® library preparation yield reliable results. Availability and Implementation: Datasets, binaries and usage instructions are available under http://all-food-seq.sourceforge.net. Raw data is available at NCBI's SRA with accession number PRJNA271645. Contact: hankeln@uni-mainz.de. Supplementary information: Supplementary data are available at Bioinformatics online. [Mh] Termos MeSH primário: Microbiologia de Alimentos/métodos Metagenômica/métodos Análise de Sequência de DNA/métodos Software [Mh] Termos MeSH secundário: Sequenciamento de Nucleotídeos em Larga Escala/métodos [Pt] Tipo de publicação: JOURNAL ARTICLE [Em] Mês de entrada: 1801 [Cu] Atualização por classe: 180308 [Lr] Data última revisão: 180308 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 170429 [St] Status: MEDLINE [do] DOI: 10.1093/bioinformatics/btw822

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[PMID]: 29246109 [Au] Autor: Martorell-Marugan J; Toro-Dominguez D; Alarcon-Riquelme ME; Carmona-Saez P [Ad] Endereço: Bioinformatics Unit, Centre for Genomics and Oncological Research (GENYO), Granada, Spain. [Ti] Título: MetaGenyo: a web tool for meta-analysis of genetic association studies. [So] Source: BMC Bioinformatics;18(1):563, 2017 Dec 16. [Is] ISSN: 1471-2105 [Cp] País de publicação: England [La] Idioma: eng [Ab] Resumo: BACKGROUND: Genetic association studies (GAS) aims to evaluate the association between genetic variants and phenotypes. In the last few years, the number of this type of study has increased exponentially, but the results are not always reproducible due to experimental designs, low sample sizes and other methodological errors. In this field, meta-analysis techniques are becoming very popular tools to combine results across studies to increase statistical power and to resolve discrepancies in genetic association studies. A meta-analysis summarizes research findings, increases statistical power and enables the identification of genuine associations between genotypes and phenotypes. Meta-analysis techniques are increasingly used in GAS, but it is also increasing the amount of published meta-analysis containing different errors. Although there are several software packages that implement meta-analysis, none of them are specifically designed for genetic association studies and in most cases their use requires advanced programming or scripting expertise. RESULTS: We have developed MetaGenyo, a web tool for meta-analysis in GAS. MetaGenyo implements a complete and comprehensive workflow that can be executed in an easy-to-use environment without programming knowledge. MetaGenyo has been developed to guide users through the main steps of a GAS meta-analysis, covering Hardy-Weinberg test, statistical association for different genetic models, analysis of heterogeneity, testing for publication bias, subgroup analysis and robustness testing of the results. CONCLUSIONS: MetaGenyo is a useful tool to conduct comprehensive genetic association meta-analysis. The application is freely available at http://bioinfo.genyo.es/metagenyo/ . [Mh] Termos MeSH primário: Estudos de Associação Genética/métodos Internet Metagenômica/métodos Software [Mh] Termos MeSH secundário: Seres Humanos [Pt] Tipo de publicação: JOURNAL ARTICLE; META-ANALYSIS [Em] Mês de entrada: 1803 [Cu] Atualização por classe: 180306 [Lr] Data última revisão: 180306 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 171217 [St] Status: MEDLINE [do] DOI: 10.1186/s12859-017-1990-4

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[PMID]: 28460196 [Au] Autor: Warinner C; Herbig A; Mann A; Fellows Yates JA; Weiß CL; Burbano HA; Orlando L; Krause J [Ad] Endereço: Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; email: warinner@shh.mpg.de. [Ti] Título: A Robust Framework for Microbial Archaeology. [So] Source: Annu Rev Genomics Hum Genet;18:321-356, 2017 Aug 31. [Is] ISSN: 1545-293X [Cp] País de publicação: United States [La] Idioma: eng [Ab] Resumo: Microbial archaeology is flourishing in the era of high-throughput sequencing, revealing the agents behind devastating historical plagues, identifying the cryptic movements of pathogens in prehistory, and reconstructing the ancestral microbiota of humans. Here, we introduce the fundamental concepts and theoretical framework of the discipline, then discuss applied methodologies for pathogen identification and microbiome characterization from archaeological samples. We give special attention to the process of identifying, validating, and authenticating ancient microbes using high-throughput DNA sequencing data. Finally, we outline standards and precautions to guide future research in the field. [Mh] Termos MeSH primário: Archaea/isolamento & purificação Bactérias/isolamento & purificação DNA Antigo/análise Metagenômica/métodos Microbiota/genética Análise de Sequência de DNA/métodos [Mh] Termos MeSH secundário: Archaea/genética Arqueologia/métodos Bactérias/genética Genoma Arqueal Genoma Bacteriano Seres Humanos [Pt] Tipo de publicação: JOURNAL ARTICLE; REVIEW [Nm] Nome de substância: 0 (DNA, Ancient) [Em] Mês de entrada: 1710 [Cu] Atualização por classe: 180228 [Lr] Data última revisão: 180228 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 170502 [St] Status: MEDLINE [do] DOI: 10.1146/annurev-genom-091416-035526

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[PMID]: 29232688 [Au] Autor: Raskina O [Ad] Endereço: Institute of Evolution, University of Haifa, Haifa, Israel. [Ti] Título: Genotype- and Cell-Specific Dynamics of Tandem Repeat Patterns in Aegilops speltoides Tausch (Poaceae, Triticeae). [So] Source: Cytogenet Genome Res;153(2):105-116, 2017. [Is] ISSN: 1424-859X [Cp] País de publicação: Switzerland [La] Idioma: eng [Ab] Resumo: In wild plant populations, chromosome rearrangements lead to the wide intraspecific polymorphisms in the abundance and patterns of highly repetitive DNA. However, despite the large amount of accumulated data, the impact of the complex repetitive DNA fraction on genome reorganization and functioning and the mechanisms balancing and maintaining the structural integrity of the genome are not fully understood. Homologous recombination is thought to play a key role in both genome reshuffling and stabilization, while the contribution of nonhomologous recombination seems to be undervalued. Here, tandem repeat patterns and dynamics during pollen mother cell development were addressed, with a focus on the meiotic recombination that determines chromosome/genome repatterning and stabilization under cross-pollination and artificial hybridization in wild goatgrass, Aegilops speltoides. Native plants from contrasting allopatric populations and artificially created intraspecific hybrids were investigated using a FISH approach. Cytogenetic analysis uncovered a wide spectrum of genotype- and cell-specific chromosomal rearrangements, suggesting intensive repatterning of both parental and hybrid genomes. The data obtained provide evidence that repetitive elements serve as overabundant and ubiquitous resources for maintaining chromosome architecture/genome integrity through homologous and nonhomologous recombination at the intraorganismal level, and genotype-specific repatterning underlies intrapopulation polymorphisms and intraspecific diversification in the wild. [Mh] Termos MeSH primário: Cromossomos de Plantas/genética DNA de Plantas/genética Poaceae/genética Sequências de Repetição em Tandem/genética [Mh] Termos MeSH secundário: Cromossomos de Plantas/ultraestrutura Cruzamentos Genéticos Genoma de Planta Genótipo Recombinação Homóloga Hibridização Genética Hibridização in Situ Fluorescente Meiose Metagenômica Polimorfismo Genético Turquia [Pt] Tipo de publicação: JOURNAL ARTICLE [Nm] Nome de substância: 0 (DNA, Plant) [Em] Mês de entrada: 1802 [Cu] Atualização por classe: 180220 [Lr] Data última revisão: 180220 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 171213 [St] Status: MEDLINE [do] DOI: 10.1159/000484917

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[PMID]: 28467925 [Au] Autor: Loomba R; Seguritan V; Li W; Long T; Klitgord N; Bhatt A; Dulai PS; Caussy C; Bettencourt R; Highlander SK; Jones MB; Sirlin CB; Schnabl B; Brinkac L; Schork N; Chen CH; Brenner DA; Biggs W; Yooseph S; Venter JC; Nelson KE [Ad] Endereço: NAFLD Research Center, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Division of Epidemiology, Department of Family and Preventive Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Division of Gastroenterology, Department of Medicine, Uni [Ti] Título: Gut Microbiome-Based Metagenomic Signature for Non-invasive Detection of Advanced Fibrosis in Human Nonalcoholic Fatty Liver Disease. [So] Source: Cell Metab;25(5):1054-1062.e5, 2017 May 02. [Is] ISSN: 1932-7420 [Cp] País de publicação: United States [La] Idioma: eng [Ab] Resumo: The presence of advanced fibrosis in nonalcoholic fatty liver disease (NAFLD) is the most important predictor of liver mortality. There are limited data on the diagnostic accuracy of gut microbiota-derived signature for predicting the presence of advanced fibrosis. In this prospective study, we characterized the gut microbiome compositions using whole-genome shotgun sequencing of DNA extracted from stool samples. This study included 86 uniquely well-characterized patients with biopsy-proven NAFLD, of which 72 had mild/moderate (stage 0-2 fibrosis) NAFLD, and 14 had advanced fibrosis (stage 3 or 4 fibrosis). We identified a set of 40 features (p < 0.006), which included 37 bacterial species that were used to construct a Random Forest classifier model to distinguish mild/moderate NAFLD from advanced fibrosis. The model had a robust diagnostic accuracy (AUC 0.936) for detecting advanced fibrosis. This study provides preliminary evidence for a fecal-microbiome-derived metagenomic signature to detect advanced fibrosis in NAFLD. [Mh] Termos MeSH primário: Bactérias/isolamento & purificação Microbioma Gastrointestinal Cirrose Hepática/microbiologia Hepatopatia Gordurosa não Alcoólica/microbiologia [Mh] Termos MeSH secundário: Adulto Idoso Bactérias/genética Fezes/microbiologia Feminino Seres Humanos Cirrose Hepática/diagnóstico Masculino Metagenômica/métodos Meia-Idade Hepatopatia Gordurosa não Alcoólica/diagnóstico Prognóstico Estudos Prospectivos [Pt] Tipo de publicação: JOURNAL ARTICLE [Em] Mês de entrada: 1802 [Cu] Atualização por classe: 180219 [Lr] Data última revisão: 180219 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 170504 [St] Status: MEDLINE

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[PMID]: 29371626 [Au] Autor: Carradec Q; Pelletier E; Da Silva C; Alberti A; Seeleuthner Y; Blanc-Mathieu R; Lima-Mendez G; Rocha F; Tirichine L; Labadie K; Kirilovsky A; Bertrand A; Engelen S; Madoui MA; Méheust R; Poulain J; Romac S; Richter DJ; Yoshikawa G; Dimier C; Kandels-Lewis S; Picheral M; Searson S; Jaillon O; Aury JM; Karsenti E; Sullivan MB; Sunagawa S; Bork P; Not F; Hingamp P; Raes J; Guidi L; Ogata H; de Vargas C; Iudicone D; Bowler C; Wincker P; Tara Oceans Coordinators [Ad] Endereço: CEA - Institut de Biologie François Jacob, Genoscope, Evry, 91057, France. [Ti] Título: A global ocean atlas of eukaryotic genes. [So] Source: Nat Commun;9(1):373, 2018 01 25. [Is] ISSN: 2041-1723 [Cp] País de publicação: England [La] Idioma: eng [Ab] Resumo: While our knowledge about the roles of microbes and viruses in the ocean has increased tremendously due to recent advances in genomics and metagenomics, research on marine microbial eukaryotes and zooplankton has benefited much less from these new technologies because of their larger genomes, their enormous diversity, and largely unexplored physiologies. Here, we use a metatranscriptomics approach to capture expressed genes in open ocean Tara Oceans stations across four organismal size fractions. The individual sequence reads cluster into 116 million unigenes representing the largest reference collection of eukaryotic transcripts from any single biome. The catalog is used to unveil functions expressed by eukaryotic marine plankton, and to assess their functional biogeography. Almost half of the sequences have no similarity with known proteins, and a great number belong to new gene families with a restricted distribution in the ocean. Overall, the resource provides the foundations for exploring the roles of marine eukaryotes in ocean ecology and biogeochemistry. [Mh] Termos MeSH primário: Organismos Aquáticos Eucariotos/genética Células Eucarióticas/metabolismo Metagenoma Filogenia Zooplâncton/genética [Mh] Termos MeSH secundário: Sequência de Aminoácidos Animais Atlas como Assunto Bactérias/classificação Bactérias/genética Biodiversidade Ecossistema Eucariotos/classificação Células Eucarióticas/citologia Metagenômica/métodos Oceanos e Mares Fitoplâncton/classificação Fitoplâncton/genética Água do Mar Vírus/classificação Vírus/genética Zooplâncton/classificação [Pt] Tipo de publicação: JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T [Em] Mês de entrada: 1802 [Cu] Atualização por classe: 180215 [Lr] Data última revisão: 180215 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 180127 [St] Status: MEDLINE [do] DOI: 10.1038/s41467-017-02342-1

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[PMID]: 29293631 [Au] Autor: Villegas LEM; Campolina TB; Barnabe NR; Orfano AS; Chaves BA; Norris DE; Pimenta PFP; Secundino NFC [Ad] Endereço: Laboratory of Medical Entomology, René Rachou Research Centre-FIOCRUZ, Minas Gerais, Brazil. [Ti] Título: Zika virus infection modulates the bacterial diversity associated with Aedes aegypti as revealed by metagenomic analysis. [So] Source: PLoS One;13(1):e0190352, 2018. [Is] ISSN: 1932-6203 [Cp] País de publicação: United States [La] Idioma: eng [Ab] Resumo: Zika is a re-emerging infection that has been considered a major threat to global public health. Currently at least 100 countries are at risk of Zika virus (ZIKV) transmission. Aedes aegypti is the main mosquito vector in the Americas. This vector is exposed to, and interacts symbiotically with a variety of microorganisms in its environment, which may result in the formation of a lifetime association. Here, the unknown effect that ZIKV exerts on the dynamic bacterial community harbored by this mosquito vector was investigated using a metagenomic analysis of its microbiota. Groups of Ae. aegypti were experimentally fed on sugar, blood and blood mixed with ZIKV, and held for 3 to 7 days after blood meal and eggs development respectively. The infected groups were processed by qPCR to confirm the presence of ZIKV. All groups were analyzed by metagenomics (Illumina Hiseq Sequencing) and 16S rRNA amplicon sequences were obtained to create bacterial taxonomic profiles. A core microbiota and exclusive bacterial taxa were identified that incorporate 50.5% of the predicted reads from the dataset, with 40 Gram-negative and 9 Gram-positive families. To address how ZIKV invasion may disturb the ecological balance of the Ae. aegypti microbiota, a CCA analysis coupled with an explanatory matrix was performed to support the biological interpretation of shifts in bacterial signatures. Two f-OTUs appeared as potential biomarkers of ZIKV infection: Rhodobacteraceae and Desulfuromonadaceae. Coincidentally, both f-OTUs were exclusively present in the ZIKV- infected blood-fed and ZIKV- infected gravid groups. In conclusion, this study shows that bacterial symbionts act as biomarkers of the insect physiological states and how they respond as a community when ZIKV invades Ae. aegypti. Basic knowledge of local haematophagous vectors and their associated microbiota is relevant when addressing transmission of vector-borne infectious diseases in their regional surroundings. [Mh] Termos MeSH primário: Aedes/microbiologia Bactérias/classificação Biodiversidade Metagenômica Infecção pelo Zika virus/microbiologia [Mh] Termos MeSH secundário: Aedes/virologia Animais Bactérias/genética Sequenciamento de Nucleotídeos em Larga Escala Mosquitos Vetores RNA Ribossômico 16S/genética [Pt] Tipo de publicação: JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T [Nm] Nome de substância: 0 (RNA, Ribosomal, 16S) [Em] Mês de entrada: 1802 [Cu] Atualização por classe: 180215 [Lr] Data última revisão: 180215 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 180103 [St] Status: MEDLINE [do] DOI: 10.1371/journal.pone.0190352

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[PMID]: 29293506 [Au] Autor: Choi JE; Nguyen CM; Lee B; Park JH; Oh JY; Choi JS; Kim JC; Song JK [Ad] Endereço: Research Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), Daejeon, Republic of Korea. [Ti] Título: Isolation and characterization of a novel metagenomic enzyme capable of degrading bacterial phytotoxin toxoflavin. [So] Source: PLoS One;13(1):e0183893, 2018. [Is] ISSN: 1932-6203 [Cp] País de publicação: United States [La] Idioma: eng [Ab] Resumo: Toxoflavin, a 7-azapteridine phytotoxin produced by the bacterial pathogens such as Burkholderia glumae and Burkholderia gladioli, has been known as one of the key virulence factors in crop diseases. Because the toxoflavin had an antibacterial activity, a metagenomic E. coli clone capable of growing well in the presence of toxoflavin (30 µg/ml) was isolated and the first metagenome-derived toxoflavin-degrading enzyme, TxeA of 140 amino acid residues, was identified from the positive E. coli clone. The conserved amino acids for metal-binding and extradiol dioxygenase activity, Glu-12, His-8 and Glu-130, were revealed by the sequence analysis of TxeA. The optimum conditions for toxoflavin degradation were evaluated with the TxeA purified in E. coli. Toxoflavin was totally degraded at an initial toxoflavin concentration of 100 µg/ml and at pH 5.0 in the presence of Mn2+, dithiothreitol and oxygen. The final degradation products of toxoflavin and methyltoxoflavin were fully identified by MS and NMR as triazines. Therefore, we suggested that the new metagenomic enzyme, TxeA, provided the clue to applying the new metagenomic enzyme to resistance development of crop plants to toxoflavin-mediated disease as well as to biocatalysis for Baeyer-Villiger type oxidation. [Mh] Termos MeSH primário: Toxinas Bacterianas/metabolismo Burkholderia/metabolismo Enzimas/metabolismo Metagenômica Pirimidinonas/metabolismo Triazinas/metabolismo [Mh] Termos MeSH secundário: Sequência de Aminoácidos Homologia de Sequência de Aminoácidos [Pt] Tipo de publicação: JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T [Nm] Nome de substância: 0 (Bacterial Toxins); 0 (Enzymes); 0 (Pyrimidinones); 0 (Triazines); 5N5YI4IP1P (toxoflavin) [Em] Mês de entrada: 1802 [Cu] Atualização por classe: 180215 [Lr] Data última revisão: 180215 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 180103 [St] Status: MEDLINE [do] DOI: 10.1371/journal.pone.0183893

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[PMID]: 28451970 [Au] Autor: Silva GGZ; Lopes FAC; Edwards RA [Ad] Endereço: Computational Science Research Center, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA. [Ti] Título: An Agile Functional Analysis of Metagenomic Data Using SUPER-FOCUS. [So] Source: Methods Mol Biol;1611:35-44, 2017. [Is] ISSN: 1940-6029 [Cp] País de publicação: United States [La] Idioma: eng [Ab] Resumo: One of the main goals in metagenomics is to identify the functional profile of a microbial community from unannotated shotgun sequencing reads. Functional annotation is important in biological research because it enables researchers to identify the abundance of functional genes of the organisms present in the sample, answering the question, "What can the organisms in the sample do?" Most currently available approaches do not scale with increasing data volumes, which is important because both the number and lengths of the reads provided by sequencing platforms keep increasing. Here, we present SUPER-FOCUS, SUbsystems Profile by databasE Reduction using FOCUS, an agile homology-based approach using a reduced reference database to report the subsystems present in metagenomic datasets and profile their abundances. SUPER-FOCUS was tested with real metagenomes, and the results show that it accurately predicts the subsystems present in the profiled microbial communities, is computationally efficient, and up to 1000 times faster than other tools. SUPER-FOCUS is freely available at http://edwards.sdsu.edu/SUPERFOCUS . [Mh] Termos MeSH primário: Biologia Computacional/métodos Metagenoma/genética Metagenômica/métodos [Mh] Termos MeSH secundário: Bases de Dados Genéticas [Pt] Tipo de publicação: JOURNAL ARTICLE [Em] Mês de entrada: 1802 [Cu] Atualização por classe: 180212 [Lr] Data última revisão: 180212 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 170429 [St] Status: MEDLINE [do] DOI: 10.1007/978-1-4939-7015-5_4

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[PMID]: 28451969 [Au] Autor: Sharifi F; Ye Y [Ad] Endereço: School of Informatics and Computing, Indiana University, 150 S. Woodlawn Ave., Bloomington, IN, 47405, USA. [Ti] Título: From Gene Annotation to Function Prediction for Metagenomics. [So] Source: Methods Mol Biol;1611:27-34, 2017. [Is] ISSN: 1940-6029 [Cp] País de publicação: United States [La] Idioma: eng [Ab] Resumo: Microbes play important roles in almost every aspect of life, including human health and diseases. Facilitated by the rapid development of sequencing technologies, metagenomics research has accelerated the accumulation of genomic sequences of microbial species that had been inaccessible before. Analysis of the metagenomic sequencing data can reveal not only the species but also the functional composition of microbial communities. Here, we report a pipeline for functional annotation of metagenomic datasets. The pipeline is built from several programs that we have developed for metagenomic sequence analysis including a protein-coding gene predictor for short reads (or contigs) and a fast similarity search tool. Given a metagenomic dataset, the pipeline reports putative protein-coding genes (or gene fragments) and functional annotations of the genes in Gene Ontology (GO) terms and Enzyme Commission (EC) numbers, and potential metabolic pathways that are likely encoded by the metagenome. Fun4Me is available for download at https://sourceforge.net/projects/fun4me . [Mh] Termos MeSH primário: Metagenômica/métodos [Mh] Termos MeSH secundário: Algoritmos Metagenoma/genética Anotação de Sequência Molecular Análise de Sequência de DNA [Pt] Tipo de publicação: JOURNAL ARTICLE [Em] Mês de entrada: 1802 [Cu] Atualização por classe: 180212 [Lr] Data última revisão: 180212 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 170429 [St] Status: MEDLINE [do] DOI: 10.1007/978-1-4939-7015-5_3

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