February 2016
Metagenomics uncovers gaps in amplicon-based detection of microbial diversity
Eloe-Fadrosh EA, Ivanova NN, Woyke T, Kyrpides NC. Nat Microbiol. 2016. doi: 10.1038/nmicrobiol.2015.32.
COMMENT: In this publication the authors compared SSU rRNA gene sequences (³ 1000 bp) with commonly used PCR primer sets and generated a weighted score based on the number of mismatches. The results showed that at least 10% of environmental... + info
SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data.
Silva GG, Green KT, Dutilh BE, Edwards RA. Bioinformatics. Feb 2016. doi: 10.1093/bioinformatics/btv584.
COMMENT: In this publication a tool for shotgun metagenomics is described: SUPER-FOCUS. It is oriented to functional profiling. The meaning of its name is SUbsystems Profile by databasE Reduction using FOCUS, because it is based in a similarity-based... + info
Biogeography of a human oral microbiome at the micron scale.
Mark Welch JL, Rossetti BJ, Rieken CW, Dewhirst FE, Borisy GG. Proc Natl Acad Sci U S A. Feb 2016. doi: 10.1073/pnas.1522149113.
COMMENT: This was a surprising publication for me. It includes amazing and beautiful images about the spatial organization of a natural human oral microbiome at the micron scale (using spectral imaging fluorescence in situ... + info
