• Aucun résultat trouvé

: Classifications et salaires minimum hiérarchiques des personnels enseignant hors

A partir dos dados analisados, pode-se afirmar que o programa VirFinder demonstrou um melhor desempenho quanto a performance de tempo de processamento das amostras e de identificação de bacteriófagos nas amostras ambientais e na amostra controle, quando comparados com os programas MARVEL e VirSorter

Além disso, o tipo de ambiente e o preparo da amostra se demonstraram como fatores importantes na capacidade de identificação destes fagos e consequentemente no resultado final obtido pelo programa. Com isso, para uma melhor interpretação do ambiente os programas devem ser utilizados de forma complementar, já que os três foram capazes de identificar bacteriófagos exclusivos em suas análises.

Neste trabalho, o VirFinder apresentou um melhor desempenho quanto a taxa de identificação, sensibilidade e tempo de processamento. Dessa forma, o próximo passo é a elaboração de um pipeline para automatização da análise ambiental com esse programa.

Novos estudos devem ser realizados para desenvolver novos programas para a identificação de bacteriófagos com estratégias de identificação distintas para melhorar a capacidade de identificação de novos fagos com potencial biotecnológico a partir de dados metagenômicos.

REFERÊNCIAS

ABEDON, S. T.; DUFFY, S.; TURNER, P. E. Bacteriophage Ecology. In: Encyclopedia of Microbiology. San Diego: Elsevier, 2009.

ACKERMANN, H.-W. Frequency of morphological phage descriptions in the year 2000. Archives of Virology, v. 146, n. 5, p. 843–857, 29 maio 2001.

ACKERMANN, H.-W. Phage Classification and Characterization. In: CLOKIE, M. R. J.; KROPINSKI, A. M. (Eds.). Bacteriophages. Totowa, NJ: Humana Press, 2009. v. 501.

AJAMI, N.J.; PETROSINO, J.F.. Enteric Viral Metagenomics. Viral Gastroenteritis, [S.L.], p. 523-533, 2016.

AKHTAR, Iqra Naveed. Viral genetics and structure. Dengue Virus Disease, [S.L.], p. 85-113, 2020.

AMGARTEN, D. et al. MARVEL, a Tool for Prediction of Bacteriophage Sequences in Metagenomic Bins. Frontiers in Genetics, v. 9, p. 304, 7 ago. 2018.

ANDREWS, S. FastQC: A Quality Control Tool for High Throughput Sequence Data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 2010.

ARYA, Pooja; RAVINDRA. Metagenomics based approach to reveal the secrets of unculturable microbial diversity from aquatic environment. Recent Advancements In Microbial Diversity, [S.L.], p. 537-559, 2020.

BOLGER, Anthony M.; LOHSE, Marc; USADEL, Bjoern. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, [s.l.], v. 30, n. 15, p.2114-2120, 1 abr. 2014.

BUSHNELL, Brian. BBMap: A Fast, Accurate, Splice-Aware Aligner. United States: N. p., 2014.

CAMACHO, Christiam; COULOURIS, George; AVAGYAN, Vahram; MA, Ning; PAPADOPOULOS, Jason; BEALER, Kevin; MADDEN, Thomas L. BLAST+: architecture and applications. Bmc Bioinformatics, [S.L.], v. 10, n. 1, p. 421-431, 2009.

49

CHALLIS R. rjchallis/assembly-stats17.02.Zenodo, 2014, doi:10.5281/zenodo.322347.

CHEN, Jianguo; LI, Kenli; TANG, Zhuo; BILAL, Kashif; YU, Shui; WENG, Chuliang; LI, Keqin. A Parallel Random Forest Algorithm for Big Data in a Spark Cloud Computing Environment. Ieee Transactions On Parallel And Distributed Systems, [S.L.], v. 28, n. 4, p. 919-933, 1 abr. 2017

CHIANG, Yin Ning; PENADÉS, José R.; CHEN, John. Genetic transduction by phages and chromosomal islands: The new and noncanonical. Plos Pathogens, [s.l.], v. 15, n. 8, p.1-7, 8 ago. 2019.

COBIÁN GÜEMES, A. G. et al. Viruses as Winners in the Game of Life. Annual Review of Virology, v. 3, n. 1, p. 197–214, 29 set. 2016.

COORDINATORS, Ncbi Resource. Database resources of the National Center for Biotechnology Information. Nucleic Acids Research, [s.l.], v. 44, n. 1, p. 7-19, 28 nov. 2015.

DAFALE, N. A. et al. Bacteriophage Diversity in Different Habitats and Their Role in Pathogen Control. In: KALIA, V. C. (Ed.). Microbial Factories. New Delhi: Springer India, 2015.

DION, Moïra B.; OECHSLIN, Frank; MOINEAU, Sylvain. Phage diversity, genomics and phylogeny. Nature Reviews Microbiology, [S.L.], v. 18, n. 3, p. 125-138, 3 fev. 2020.

DUCKWORTH, D H. "Who discovered bacteriophage?". Bacteriol Rev., Ontario, v. 40, n. 4, p. 793-802, out. 1976.

EDDY, Sean R.. Accelerated Profile HMM Searches. Plos Computational Biology, [s.l.], v. 7, n. 10, p. 1-10, 20 out. 2011.

EDWARDS, R. A.; ROHWER, F. Viral metagenomics. Nature Reviews Microbiology, v. 3, n. 6, p. 504–510, maio 2005.

EWING, Brent; HILLIER, Ladeana; WENDL, Michael C.; GREEN, Phil. Base-Calling of Automated Sequencer Traces UsingPhred. I. Accuracy Assessment. Genome Research, [s.l.], v. 8, n. 3, p. 175-185, 1 mar. 1998.

32, n. 9, p. 1405-1407, 5 jan. 2016.

GELDERBLOM, H. R. Structure and Classification of Virus. In: Baron S, editor. Medical Microbiology. 4 th edition. Galveston : University of Texas Medical Branch at Galveston, 1996.

GHURYE, Jay S.; CEPEDA-ESPINOZA, Victoria; POP, Mihai. Metagenomic

Assembly: Overview, Challenges and Applications. Yale J Biol Med, New Haven, v. 3, n. 89, p. 353-362, set. 2016.

HAQ, Irshad Ul; CHAUDHRY, Waqas Nasir; AKHTAR, Maha Nadeem; ANDLEEB, Saadia; QADRI, Ishtiaq. Bacteriophages and their implications on future

biotechnology: a review. Virology Journal, [s.l.], v. 9, n. 1, p.1-8, 10 jan. 2012. HARADA, Liliam K.; SILVA, Erica C.; CAMPOS, Welida F.; FIOL, Fernando S. del; VILA, Marta; DąBROWSKA, Krystyna; KRYLOV, Victor N.; BALCÃO, Victor M.. Biotechnological applications of bacteriophages: State of the art. Microbiological Research, [s.l.], v. 212-213, p.38-58, jul. 2018.

HATFULL, Graham F.; JACOBS-SERA, Deborah; LAWRENCE, Jeffrey G.; POPE, Welkin H.; RUSSELL, Daniel A.; KO, Ching-Chung; WEBER, Rebecca J.; PATEL, Manisha C.; GERMANE, Katherine L.; EDGAR, Robert H.. Comparative Genomic Analysis of 60 Mycobacteriophage Genomes: genome clustering, gene acquisition, and gene size. Journal Of Molecular Biology, [S.L.], v. 397, n. 1, p. 119-143, mar. 2010.

HAYES, S. et al. Metagenomic Approaches to Assess Bacteriophages in Various Environmental Niches. Viruses, v. 9, n. 6, p. 127, 24 maio 2017.

HUANG, W. et al. ART: a next-generation sequencing read simulator. Bioinformatics, v. 28, n. 4, p. 593–594, 15 fev. 2012.

HURWITZ, Bonnie L.; SULLIVAN, Matthew B.. The Pacific Ocean Virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology. Plos One, [S.L.], v. 8, n. 2, p. 1-12, 28 fev. 2013.

ILLUMINA, INC. TECHNICAL NOTE: SEQUENCING: Quality Scores for Next- Generation Sequencing Assessing sequencing accuracy using Phred quality scoring. San Diego: Illumina, Inc., 2011.

LABRIE, Simon J.; DUPUIS, Marie-Ève; TREMBLAY, Denise M.; PLANTE, Pier-Luc; CORBEIL, Jacques; MOINEAU, Sylvain. A New Microviridae Phage Isolated from a

51

Failed Biotechnological Process Driven by Escherichia coli. Applied And Environmental Microbiology, [S.L.], v. 80, n. 22, p. 6992-7000, 5 set. 2014. LEINONEN, R.; SUGAWARA, H.; SHUMWAY, M.. The Sequence Read Archive. Nucleic Acids Research, [s.l.], v. 39, n. , p.19-21, 9 nov. 2010.

LEINONEN, R.; AKHTAR, R.; BIRNEY, E.; BOWER, L.; CERDENO-TARRAGA, A.; CHENG, Y.; CLELAND, I.; FARUQUE, N.; GOODGAME, N.; GIBSON, R.. The European Nucleotide Archive. Nucleic Acids Research, [s.l.], v. 39, n. , p. 28-31, 23 out. 2010.

LI, H.; DURBIN, R.. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, [s.l.], v. 25, n. 14, p. 1754-1760, 18 maio 2009.

LI, H.; HANDSAKER, B.; WYSOKER, A.; FENNELL, T.; RUAN, J.; HOMER, N.; MARTH, G.; ABECASIS, G.; DURBIN, R.. The Sequence Alignment/Map format and SAMtools. Bioinformatics, [s.l.], v. 25, n. 16, p. 2078-2079, 8 jun. 2009

LINDBERG, Alf Anton. Bacteriophage Receptors. Annual Review Of Microbiology, [s.l.], v. 27, n. 1, p.205-241, out. 1973.

LU, Shuguang; LE, Shuai; TAN, Yinling; ZHU, Junmin; LI, Ming; RAO, Xiancai; ZOU, Lingyun; LI, Shu; WANG, Jing; JIN, Xiaolin. Genomic and Proteomic Analyses of the Terminally Redundant Genome of the Pseudomonas aeruginosa Phage PaP1: establishment of genus pap1-like phages. Plos One, [S.L.], v. 8, n. 5, p. 29-33, 13 maio 2013.

LYNE, J.. Bacteriophage | Technological Importance in the Diary Industry. Encyclopedia Of Dairy Sciences, [S.L.], p. 439-444, 2011.

MADIGAN, M. T. et al. Brock biology of microorganisms. Fourteenth edition ed. Boston: Pearson, 2016. v. 14.

MARINTCHEVA, Boriana. Introduction to Viral Structure, Diversity and Biology: the fascinating world of viruses. bridgew rev 2013;32(2). Harnessing The Power Of Viruses, [S.L.], p. 1-26, 2018.

MANSOUR, Nahla M. Bacteriophages are natural gift, could we pay further attention! Journal Of Food Microbiology, London, v. 1, p.22-23, set. 2017.

MARTI, E.; VARIATZA, E.; BALCAZAR, J. L. The role of aquatic ecosystems as reservoirs of antibiotic resistance. Trends in Microbiology, v. 22, n. 1, p. 36–41, jan. 2014.

NAKAOKA, Shinji; OTA, Keisuke H.. An information and statistical analysis pipeline for microbial metagenomic sequencing data. Handbook Of Statistics, [S.L.], p. 67- 80, 2020.

NURK, Sergey; MELESHKO, Dmitry; KOROBEYNIKOV, Anton; PEVZNER, Pavel A.. MetaSPAdes: a new versatile metagenomic assembler. Genome Research, [s.l.], v. 27, n. 5, p.824-834, 15 mar. 2017.

OBENG, N.; PRATAMA, A. A.; ELSAS, J. D. VAN. The Significance of Mutualistic Phages for Bacterial Ecology and Evolution. Trends in Microbiology, v. 24, n. 6, p. 440–449, jun. 2016.

Oliveros, J.C., Venny. An interactive tool for comparing lists with Venn's diagrams. https://bioinfogp.cnb.csic.es/tools/venny/index.html, 2015.

PARKS, Donovan H.; IMELFORT, Michael; SKENNERTON, Connor T.; HUGENHOLTZ, Philip; TYSON, Gene W.. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. :

assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Research, [s.l.], v. 25, n. 7, p. 1043-1055, 14 maio 2015. PARMAR, K. et al. An Insight into Phage Diversity at Environmental Habitats using Comparative Metagenomics Approach. Current Microbiology, v. 75, n. 2, p. 132– 141, set. 2017.

PATEL, Manvendra; CHAUBEY, Abhishek Kumar; PITTMAN, Charles U.; MLSNA, Todd; MOHAN, Dinesh. Coronavirus (SARS-CoV-2) in the Environment: occurrence, persistence, analysis in aquatic systems and possible management. Science Of The Total Environment, [S.L.], p. 1-68, out. 2020.

POP, M.. Genome assembly reborn: recent computational challenges. Briefings In Bioinformatics, [S.L.], v. 10, n. 4, p. 354-366, 29 maio 2009.

QUINCE, Christopher; WALKER, Alan W; SIMPSON, Jared T; LOMAN, Nicholas J; SEGATA, Nicola. Shotgun metagenomics, from sampling to analysis. Nature Biotechnology, [S.L.], v. 35, n. 9, p. 833-844, set. 2017

R Development Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0. 2020. Disponível em <http://www.R-project.org. >.

RAKHUBA, D. V. et al. Bacteriophage Receptors, Mechanisms of Phage Adsorption and Penetration into Host Cell. Polish Journal Of Microbiology, v. 59, n. 3, p. 145–

53

155, jul. 2010.

REN, J. et al. VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data. Microbiome, v. 5, n. 1, p. 69, dez. 2017.

ROJAS, Manuel; MONSALVE, Diana M.; PACHECO, Yovana; ACOSTA-AMPUDIA, Yeny; RAMÍREZ-SANTANA, Carolina; ANSARI, Aftab A.; GERSHWIN, M. Eric; ANAYA, Juan-Manuel. Ebola virus disease: an emerging and re-emerging viral threat. Journal Of Autoimmunity, [S.L.], v. 106, p. 1-26, jan. 2020.

ROUX, S. et al. VirSorter: mining viral signal from microbial genomic data. PeerJ, v. 3, p. e985, 28 maio 2015.

SCHOLZ, M. B.; LO, C.-C.; CHAIN, P. S. Next generation sequencing and

bioinformatic bottlenecks: the current state of metagenomic data analysis. Current Opinion in Biotechnology, v. 23, n. 1, p. 9–15, fev. 2012.

SEEMANN, T.. Prokka: rapid prokaryotic genome annotation. : rapid prokaryotic genome annotation. Bioinformatics, [s.l.], v. 30, n. 14, p. 2068-2069, 18 mar. 2014. STAATS, Charley Christian et al. Projetos Genoma. In: VERLI, Hugo.

Bioinformática da Biologia à flexibilidade. São Paulo: Sbbq, 2014.

STOREY JD, BASS AJ, DABNEY A, ROBINSON D. qvalue: Q-value estimation for false discovery rate control. R package version 2.2.2. Available from: http://github.com/jdstorey/qvalue, 2015.

SUBIRATS, J. et al. Metagenomic analysis reveals that bacteriophages are reservoirs of antibiotic resistance genes. International Journal of Antimicrobial Agents, v. 48, n. 2, p. 163–167, ago. 2016.

SUMIDA, Ciro H.. Viral diseases of crops: a critical review. Applied Plant Virology, [S.L.], p. 471-474, 2020.

TRIPATHI, Lokesh Kumar; NAILWAL, Tapan Kumar. Metagenomics: applications of functional and structural approaches and meta-omics. Recent Advancements In Microbial Diversity, [S.L.], p. 471-505, 2020.

TRINGE, S. G.; RUBIN, E. M. Metagenomics: DNA sequencing of environmental samples. Nature Reviews Genetics, v. 6, n. 11, p. 805–814, nov. 2005.

WAGNER, Glauber; JARDIM, Rodrigo; A TSCHOEKE, Diogo; LOUREIRO, Daniel R; OCAÑA, Kary Acs; RIBEIRO, Antonio Cb; EMMEL, Vanessa e; PROBST, Christian M; PITALUGA, André N; GRISARD, Edmundo C. STINGRAY: system for integrated genomic resources and analysis. Bmc Research Notes, [s.l.], v. 7, n. 1, p.132-141,

WANG, Ziye; WANG, Ying; A FUHRMAN, Jed; SUN, Fengzhu; ZHU, Shanfeng. Assessment of metagenomic assemblers based on hybrid reads of real and

simulated metagenomic sequences. Briefings In Bioinformatics, [S.L.], v. 21, n. 3, p. 777-790, 11 mar. 2019.

WEINBAUER, M. G. Ecology of prokaryotic viruses. FEMS Microbiology Reviews, v. 28, n. 2, p. 127–181, maio 2004.

WILLIAMSON, Kurt E.; FUHRMANN, Jeffry J.; WOMMACK, K. Eric; RADOSEVICH, Mark. Viruses in Soil Ecosystems: an unknown quantity within an unexplored

territory. Annual Review Of Virology, [S.L.], v. 4, n. 1, p. 201-219, 29 set. 2017. Wheeler D., Bhagwat M.. BLAST QuickStart: Example-Driven Web-Based BLAST Tutorial. In: Bergman NH, editor. Comparative Genomics: Volumes 1 and 2. Totowa (NJ): Humana Press, 2007.

Documents relatifs