Gajer, P., Brotman, R. M., Bai, G., Sakamoto, J., Schütte, U. M. E., Zhong, X., Koenig, S. S. K., et al. (2012). Temporal dynamics of the human vaginal microbiota. Science translational medicine, 4(132), 132ra52. doi:10.1126/scitranslmed.3003605 Elucidating the factors that impinge on the stability of bacterial communities in the vagina may help in predicting the risk…
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http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0050077 Abstract: The world’s oceans contain a complex mixture of micro-organisms that are for the most part, uncharacterized both genetically and biochemically. We report here a metagenomic study of the marine planktonic microbiota in which surface (mostly marine) water samples were analyzed as part of the Sorcerer II Global Ocean Sampling expedition. These samples, collected…
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Santamaria, M., Fosso, B., Consiglio, A., De Caro, G., Grillo, G., Licciulli, F., Liuni, S., et al. (2012). Reference databases for taxonomic assignment in metagenomics. Briefings in bioinformatics, 13(6), 682–695. doi:10.1093/bib/bbs036 Metagenomics is providing an unprecedented access to the environmental microbial diversity. The amplicon-based metagenomics approach involves the PCR-targeted sequencing of a genetic locus…
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DeLeon-Rodriguez, N., Lathem, T. L., Rodriguez-r, L. M., Barazesh, J. M., Anderson, B. E., Beyersdorf, A. J., Ziemba, L. D., et al. (2013). Microbiome of the upper troposphere Species composition and prevalence effects of tropical storms and atmospheric implications. PNAS, 1212089110–. doi:10.1073/pnas.1212089110 The composition and prevalence of microorganisms in the middle-to-upper troposphere (8-15 km altitude)…
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Mykytczuk, N. C., Foote, S. J., Omelon, C. R., Southam, G., Greer, C. W., & Whyte, L. G. (2013). Bacterial growth at −15 °C; molecular insights from the permafrost bacterium Planococcus halocryophilus Or1. The ISME Journal, 1–16. doi:10.1038/ismej.2013.8 Planococcus halocryophilus strain Or1, isolated from high Arctic permafrost, grows and divides at ~15 °C, the lowest…
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Meyer, F., Paarmann, D., D’Souza, M., Olson, R., Glass, E. M., Kubal, M., Paczian, T., et al. (2008).The metagenomics RAST server a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC bioinformatics, 9, 386. doi:10.1186/1471-2105-9-386 BACKGROUND: Random community genomes (metagenomes) are now commonly used to study microbes in different environments. Over the…
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Teeling, H., & Glöckner, F. O. (2012). Current opportunities and challenges in microbial metagenome analysis–a bioinformatic perspective. Briefings in bioinformatics, 13(6), 728–742. doi:10.1093/bib/bbs039 Metagenomics has become an indispensable tool for studying the diversity and metabolic potential of environmental microbes, whose bulk is as yet non-cultivable. Continual progress in next-generation sequencing allows for generating increasingly large…
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De Filippo, C., Ramazzotti, M., Fontana, P., & Cavalieri, D. (2012). Bioinformatic approaches for functional annotation and pathway inference in metagenomics data. Briefings in Bioinformatics, 13(6), 696–710. doi:10.1093/bib/bbs070 Metagenomic approaches are increasingly recognized as a baseline for understanding the ecology and evolution of microbial ecosystems.The development ofmethods for pathway inference frommetagenomics data is of paramount…
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Loman, N. J., Constantinidou, C., Chan, J. Z. M., Halachev, M., Sergeant, M., Penn, C. W., Robinson, E. R., et al. (2012). High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity. Nature reviews. Microbiology, 10(9), 599–606. doi:10.1038/nrmicro2850 Here, we take a snapshot of the high-throughput sequencing platforms, together with the relevant analytical…
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Gilbert, J. a, O’Dor, R., King, N., & Vogel, T. M. (2011). The importance of metagenomic surveys to microbial ecology: or why Darwin would have been a metagenomic scientist. Microbial informatics and experimentation, 1(1), 5. doi:10.1186/2042-5783-1-5 ABSTRACT: Scientific discovery is incremental. The Merriam-Webster definition of ‘Scientific Method’ is «principles and procedures for the systematic pursuit…
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Alcaraz, L.D., et al. (2010). Understanding the evolutionary relationships and major traits of Bacillus through comparative genomics. BMC genomics, 11(1), 332. doi:10.1186/1471-2164-11-332 BACKGROUND:The presence of Bacillus in very diverse environments reflects the versatile metabolic capabilities of a widely distributed genus. Traditional phylogenetic analysis based on limited gene sampling is not adequate for resolving the genus…
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Tettelin, H., Masignani, V., Cieslewicz, M. J., Donati, C., Medini, D., Ward, N. L., Angiuoli, S. V, et al. (2005). Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome”. Proc Natl Acad Sci U S A, 102(39), 13950–13955. Retrieved from http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16172379 The development of efficient and inexpensive genome sequencing methods…
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Konstantinidis, K. T., & Tiedje, J. M. (2007). Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. Current opinion in microbiology, 10(5), 504–9. doi:10.1016/j.mib.2007.08.006 Advancing prokaryotic taxonomy constitutes a contemporary academic challenge as well as practical necessity. Genome sequencing has greatly facilitated the evaluation of the current taxonomic system and the development…
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