| dc.creator | Carlos C. | |
| dc.creator | Castro D.B.A. | |
| dc.creator | Ottoboni L.M.M. | |
| dc.date | 2014 | |
| dc.date | 2015-06-25T17:54:52Z | |
| dc.date | 2015-11-26T14:36:35Z | |
| dc.date | 2015-06-25T17:54:52Z | |
| dc.date | 2015-11-26T14:36:35Z | |
| dc.date.accessioned | 2018-03-28T21:40:31Z | |
| dc.date.available | 2018-03-28T21:40:31Z | |
| dc.identifier | | |
| dc.identifier | Plos One. Public Library Of Science, v. 9, n. 11, p. - , 2014. | |
| dc.identifier | 19326203 | |
| dc.identifier | 10.1371/journal.pone.0111626 | |
| dc.identifier | http://www.scopus.com/inward/record.url?eid=2-s2.0-84915820087&partnerID=40&md5=acf4db65558cbd02cf1bb31664aeb9ea | |
| dc.identifier | http://www.repositorio.unicamp.br/handle/REPOSIP/86756 | |
| dc.identifier | http://repositorio.unicamp.br/jspui/handle/REPOSIP/86756 | |
| dc.identifier | 2-s2.0-84915820087 | |
| dc.identifier.uri | http://repositorioslatinoamericanos.uchile.cl/handle/2250/1248817 | |
| dc.description | By comparing the SEED and Pfam functional profiles of metagenomes of two Brazilian coral species with 29 datasets that are publicly available, we were able to identify some functions, such as protein secretion systems, that are overrepresented in the metagenomes of corals and may play a role in the establishment and maintenance of bacteria-coral associations. However, only a small percentage of the reads of these metagenomes could be annotated by these reference databases, which may lead to a strong bias in the comparative studies. For this reason, we have searched for identical sequences (99% of nucleotide identity) among these metagenomes in order to perform a reference-independent comparative analysis, and we were able to identify groups of microbial communities that may be under similar selective pressures. The identification of sequences shared among the metagenomes was found to be even better for the identification of groups of communities with similar niche requirements than the traditional analysis of functional profiles. This approach is not only helpful for the investigation of similarities between microbial communities with high proportion of unknown reads, but also enables an indirect overview of gene exchange between communities. | |
| dc.description | 9 | |
| dc.description | 11 | |
| dc.description | | |
| dc.description | | |
| dc.description | Dutilh, B.E., Schmieder, R., Nulton, J., Felts, B., Salamon, P., Referenceindependent comparative metagenomics using cross-assembly: CrAss (2012) Bioinformatics, 28, pp. 3225-3231 | |
| dc.description | Teeling, H., Glöckner, F.O., Current opportunities and challenges in microbial metagenome analysis - A bioinformatic perspective (2012) Brief Bioinform, 13, pp. 728-742 | |
| dc.description | Kloesges, T., Popa, O., Martin, W., Dagan, T., Networks of gene sharing among 329 proteobacterial genomes reveal differences in lateral gene transfer frequency at different phylogenetic depths (2010) Mol Biol Evol, 28, pp. 1057-1074 | |
| dc.description | Smillie, C.S., Smith, M.B., Friedman, J., Cordero, O.X., David, L.A., Ecology drives a global network of gene exchange connecting the human microbiome (2011) Nature, 480, pp. 241-244 | |
| dc.description | Forsberg, K.J., Reyes, A., Wang, B., Selleck, E.M., Sommer, M.O., The shared antibiotic resistome of soil bacteria and human pathogens (2012) Science, 337, pp. 1107-1111 | |
| dc.description | Schmieder, R., Edwards, R., Quality control and preprocessing of metagenomic datasets (2011) Bioinformatics, 27, pp. 863-886 | |
| dc.description | Schmieder, R., Lim, Y.W., Rohwer, F., Edwards, R., TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets (2010) BMC Bioinformatics, 11, p. 341 | |
| dc.description | Meyer, F., Paarmann, D., D'Souza, M., Olson, R., Glass, E.M., The metagenomics RAST server - A public resource for the automatic phylogenetic and functional analysis of metagenomes (2008) BMC Bioinformatics, 9, p. 386 | |
| dc.description | Lingner, T., Asshauer, K.P., Schreiber, F., Meinicke, P., CoMet - A web server for comparative functional profiling of metagenomes (2011) Nucleic Acids Res, 39, pp. W518-523 | |
| dc.description | Roux, S., Faubladier, M., Mahul, A., Paulhe, N., Bernard, A., Metavir: A web server dedicated to virome analysis (2011) Bioinformatics, 27, pp. 3074-3075 | |
| dc.description | White, J.R., Nagarajan, N., Pop, M., Statistical methods for detecting differentially abundant features in clinical metagenomic samples (2009) PLOS Comput Biol, 5, p. e1000352 | |
| dc.description | Szalay-Beko, M., Palotai, R., Szappanos, B., Kovács, I.A., Papp, B., ModuLand plug-in for Cytoscape: Determination of hierarchical layers of overlapping network modules and community centrality (2012) Bioinformatics, 28, pp. 2202-2204 | |
| dc.description | Delwart, E., Li, L., Rapidly expanding genetic diversity and host range of the Circoviridae viral family and other Rep encoding small circular ssDNA genomes (2012) Virus Res, 164, pp. 114-121 | |
| dc.description | Krupovic, M., Forterre, P., Microviridae goes temperate: Microvirus-related proviruses reside in the genomes of Bacteroidetes (2011) PLOS One, 10, p. e19893 | |
| dc.description | Labonté, J.M., Suttle, C.A., Metagenomic and whole-genome analysis reveals new lineages of gokushoviruses and biogeographic separation in the sea (2013) Front Microbiol, 4, p. 404 | |
| dc.description | Angly, F.E., Felts, B., Breitbart, M., Salamon, P., Edwards, R.A., The marine viromes of four oceanic regions (2006) PLOS Biol, 4, p. e368 | |
| dc.description | Sharp, K.H., Ritchie, K.B., Schupp, P.J., Ritson-Williams, R., Paul, V.J., Bacterial acquisition in juveniles of several broadcast spawning coral species (2010) PLOS One, 5, p. e10898 | |
| dc.description | Burke, C., Steinberg, P., Rusch, D., Kjelleberg, S., Thomas, T., Bacterial community assembly based on functional genes rather than species (2011) Proc Natl Acad Sci USA, 108, pp. 14288-14293 | |
| dc.description | Carlos, C., Torres, T.T., Ottoboni, L.M., Bacterial communities and speciesspecific associations with the mucus of Brazilian coral species (2013) Sci Rep, 2013, p. 31624 | |
| dc.description | Schöttner, S., Wild, C., Hoffmann, F., Boetius, A., Ramette, A., Spatial scales of bacterial diversity in cold-water coral reef ecosystems (2012) PLOS One, 7, p. e32093 | |
| dc.description | Schöttner, S., Hoffmann, F., Wild, C., Rapp, H.T., Boetius, A., Inter- and intra-habitat bacterial diversity associated with cold-water corals (2009) ISME J, 3, pp. 156-759 | |
| dc.description | Garcia, G.D., Gregoracci, G.B., Santos Ede, O., Meirelles, P.M., Silva, G.G., Metagenomic analysis of healthy and white plague-affected Mussismilia braziliensis corals (2013) Microb Ecol, 65, pp. 1076-1086 | |
| dc.description | Vega Thurber, R., Willner-Hall, D., Rodriguez-Mueller, B., Desnues, C., Edwards, R.A., Metagenomic analysis of stressed coral holobionts (2009) Environ Microbiol, 11, pp. 2148-2163 | |
| dc.description | Wegley, L., Edwards, R., Rodriguez-Brito, B., Liu, H., Rohwer, F., Metagenomic analysis of the microbial community associated with the coral Porites astreoides (2007) Environ Microbiol, 9, pp. 2707-2719 | |
| dc.description | Fath, M.J., Mahanty, H.K., Kolter, R., Characterization of a purF operon mutation which affects colicin v production (1989) J Bacteriol, 171, pp. 3158-3161 | |
| dc.description | Charles, H., Balmand, S., Lamelas, A., Cottret, L., Pérez-Brocal, V., A genomic reappraisal of symbiotic function in the aphid/Buchnera symbiosis: Reduced transporter sets and variable membrane organisations (2011) PLOS One, 6, p. e29096 | |
| dc.description | Gardebrecht, A., Markert, S., Sievert, S.M., Felbeck, H., Thürmer, A., Physiological homogeneity among the endosymbionts of Riftia pachyptila and Tevnia jerichonana revealed by proteogenomics (2012) ISME J, 6, pp. 766-776 | |
| dc.description | Hadjifrangiskou, M., Gu, A.P., Pinkner, J.S., Kostakioti, M., Zhang, E.W., Transposon mutagenesis identifies uropathogenic Escherichia coli biofilm factors (2012) J Bacteriol 2012, 194, pp. 6195-6205 | |
| dc.description | Breton, C., Structures and mechanisms of glycosyltransferases (2006) Glycobiology, 16, pp. 29-37 | |
| dc.description | Upreti, R.K., Kumar, M., Shankar, V., Bacterial glycoproteins: Functions, biosynthesis and applications (2003) Proteomics, 3, pp. 363-379 | |
| dc.description | Yip, E.S., Grublesky, B.T., Hussa, E.A., Visick, K.L., A novel conserved cluster of genes promotes symbiotic colonization and sigma-dependent biofilm formation by Vibrio fischeri (2005) Mol Microbiol, 57, pp. 1485-1498 | |
| dc.description | Brown Kav, A., Sasson, G., Jami, E., Doron-Faigenboim, A., Benhar, I., Insights into the bovine rumen plasmidome (2012) Proc Natl Acad Aci USA, 109, pp. 5452-5457 | |
| dc.description | Tseng, T.T., Tyler, B.M., Setubal, J.C., Protein secretion systems in bacterialhost associations, and their description in the Gene Ontology (2009) BMC Microbiol, 9, p. S2 | |
| dc.description | Gophna, U., Ron, E.Z., Graur, D., Bacterial type III secretion systems are ancient and evolved by multiple horizontal-transfer events (2003) Gene, 312, pp. 151-163 | |
| dc.description | Barret, M., Egan, F., O'Gara, F., Distribution and diversity of bacterial secretion systems across metagenomic datasets (2013) Environ Microbiol, 5, pp. 117-126 | |
| dc.description | Bondarev, V., Richter, M., Romano, S., Piel, J., Schwedt, A., The genus Pseudovibrio contains metabolically versatile bacteria adapted for symbiosis (2013) Environ Microbiol, 15, pp. 2095-2113 | |
| dc.description | Trindade-Silva, A.E., Rua, C., Silva, G.G., Dutilh, B.E., Moreira, A.P., Taxonomic and functional microbial signatures of the endemic marine sponge Arenosclera brasiliensis (2012) PLOS One, 7, p. e39905 | |
| dc.description | Turnbaugh, P.J., Hamady, M., Yatsunenko, T., Cantarel, B.L., Duncan, A., A core gut microbiome in obese and lean twins (2009) Nature, 457, pp. 480-484 | |
| dc.description | Qu, A., Brulc, J.M., Wilson, M.K., Law, B.F., Theoret, J.R., Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome (2008) PLoS One, 3, p. e2945 | |
| dc.description | Tamminen, M., Virta, M., Fani, R., Fondi, M., Large-scale analysis of plasmid relationships through gene-sharing networks (2011) Mol Biol Evol, 29, pp. 1225-1240 | |
| dc.description | McCallum, H., Harvell, D., Dobson, A., Rates of spread of marine pathogens (2003) Ecol Lett, 6, pp. 1062-1067 | |
| dc.description | Rohwer, F., Thurber, R.V., Viruses manipulate the marine environment (2009) Nature, 459, pp. 207-212 | |
| dc.description | Muniesa, M., Colomer-Lluch, M., Jofre, J., Potential impact of environmental bacteriophages in spreading antibiotic resistance genes (2013) Future Microbiol, 8, pp. 739-751 | |
| dc.description | Breitbart, M., Miyake, J.H., Rohwer, F., Global distribution of nearly identical phage-encoded DNA sequences (2004) FEMS Microbiol Lett, 236, pp. 249-256 | |
| dc.description | Short, C.M., Suttle, C.A., Nearly identical bacteriophage structural gene sequences are widely distributed in both marine and freshwater environments (2005) Appl Environ Microbiol, 71, pp. 480-486 | |
| dc.language | en | |
| dc.publisher | Public Library of Science | |
| dc.relation | PLoS ONE | |
| dc.rights | aberto | |
| dc.source | Scopus | |
| dc.title | Comparative Metagenomic Analysis Of Coral Microbial Communities Using A Reference-independent Approach | |
| dc.type | Artículos de revistas | |
