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February 2016

Metagenomics uncovers gaps in amplicon-based detection of microbial diversity
23/09/2016
Publication

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.
22/08/2016
Publication

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.
22/08/2016
Publication

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

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