Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species
作者： Serena Manara , Francesco Asnicar , Francesco Beghini , Davide Bazzani , Fabio Cumbo
DOI: 10.1186/S13059-019-1923-9
关键词: Human genetics 、 Elusimicrobia 、 Symbiosis 、 Human microbiome 、 Genetic algorithm 、 Evolutionary biology 、 Metagenomics 、 Biology 、 Microbiome 、 Genome
摘要: Humans have coevolved with microbial communities to establish a mutually advantageous relationship that is still poorly characterized and can provide a better understanding of the human microbiome. Comparative metagenomic analysis of human and non-human primate (NHP) microbiomes offers a promising approach to study this symbiosis. Very few microbial species have been characterized in NHP microbiomes due to their poor representation in the available cataloged microbial diversity, thus limiting the potential of such comparative …
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Suleyman Yildirim, Carl J. Yeoman, Maksim Sipos, Manolito Torralba, Brenda A. Wilson, Tony L. Goldberg, Rebecca M. Stumpf, Steven R. Leigh, Bryan A. White, Karen E. Nelson, Characterization of the Fecal Microbiome from Non-Human Wild Primates Reveals Species Specific Microbial Communities PLoS ONE. ,vol. 5, pp. e13963- ,(2010) , 10.1371/JOURNAL.PONE.0013963
J. G. Fox, S. R. Boutin, L. K. Handt, N. S. Taylor, S. Xu, B. Rickman, R. P. Marini, F. E. Dewhirst, B. J. Paster, S. Motzel, H. J. Klein, Isolation and Characterization of a Novel Helicobacter Species, “Helicobacter macacae,” from Rhesus Monkeys with and without Chronic Idiopathic Colitis Journal of Clinical Microbiology. ,vol. 45, pp. 4061- 4063 ,(2007) , 10.1128/JCM.01100-07
Donovan H. Parks, Michael Imelfort, Connor T. Skennerton, Philip Hugenholtz, Gene W. Tyson, CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes Genome Research. ,vol. 25, pp. 1043- 1055 ,(2015) , 10.1101/GR.186072.114
Dinghua Li, Chi-Man Liu, Ruibang Luo, Kunihiko Sadakane, Tak-Wah Lam, MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph Bioinformatics. ,vol. 31, pp. 1674- 1676 ,(2015) , 10.1093/BIOINFORMATICS/BTV033
Simon Rasmussen, Morten Erik Allentoft, Kasper Nielsen, Ludovic Orlando, Martin Sikora, Karl-Göran Sjögren, Anders Gorm Pedersen, Mikkel Schubert, Alex Van Dam, Christian Moliin Outzen Kapel, Henrik Bjørn Nielsen, Søren Brunak, Pavel Avetisyan, Andrey Epimakhov, Mikhail Viktorovich Khalyapin, Artak Gnuni, Aivar Kriiska, Irena Lasak, Mait Metspalu, Vyacheslav Moiseyev, Andrei Gromov, Dalia Pokutta, Lehti Saag, Liivi Varul, Levon Yepiskoposyan, Thomas Sicheritz-Pontén, Robert A. Foley, Marta Mirazón Lahr, Rasmus Nielsen, Kristian Kristiansen, Eske Willerslev, Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago. Cell. ,vol. 163, pp. 571- 582 ,(2015) , 10.1016/J.CELL.2015.10.009
Jasper F. W. Chan, Susanna K. P. Lau, Kelvin K. W. To, Vincent C. C. Cheng, Patrick C. Y. Woo, Kwok-Yung Yuen, Middle East Respiratory Syndrome Coronavirus: Another Zoonotic Betacoronavirus Causing SARS-Like Disease Clinical Microbiology Reviews. ,vol. 28, pp. 465- 522 ,(2015) , 10.1128/CMR.00102-14
S. Capella-Gutierrez, J. M. Silla-Martinez, T. Gabaldon, trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses Bioinformatics. ,vol. 25, pp. 1972- 1973 ,(2009) , 10.1093/BIOINFORMATICS/BTP348
Nicola Segata, Daniela Börnigen, Xochitl C. Morgan, Curtis Huttenhower, PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes Nature Communications. ,vol. 4, pp. 2304- 2304 ,(2013) , 10.1038/NCOMMS3304
Oliver Geissinger, Daniel P. R. Herlemann, Erhard Mörschel, Uwe G. Maier, Andreas Brune, The Ultramicrobacterium “Elusimicrobium minutum” gen. nov., sp. nov., the First Cultivated Representative of the Termite Group 1 Phylum Applied and Environmental Microbiology. ,vol. 75, pp. 2831- 2840 ,(2009) , 10.1128/AEM.02697-08
Howard Ochman, Michael Worobey, Chih-Horng Kuo, Jean-Bosco N. Ndjango, Martine Peeters, Beatrice H. Hahn, Philip Hugenholtz, Evolutionary Relationships of Wild Hominids Recapitulated by Gut Microbial Communities PLoS Biology. ,vol. 8, pp. e1000546- ,(2010) , 10.1371/JOURNAL.PBIO.1000546