Nice title, nice paper: Microbiome Datasets Are Compositional: And This Is Not Optional 

This seems like it is a must read for anyone working on microbiomes: Frontiers | Microbiome Datasets Are Compositional: And This Is Not Optional | Microbiology Gloor GB, Macklaim JM, Pawlowsky-Glahn V and Egozcue JJ (2017) Microbiome Datasets Are Compositional: And This Is Not Optional. Front. Microbiol. 8:2224. doi: 10.3389/fmicb.2017.02224 Summary from the paper: Datasets …

Paper of interest comparing taxonomies of SILVA, RDP, Greengenes, NCBI and OTT 

Just a quick post here.  There is a paper of interest I thought I would call attention to: Source: SILVA, RDP, Greengenes, NCBI and OTT — how do these taxonomies compare? | BMC Genomics  by Monika Balvočiūtė and Daniel H. Huson Abstract: Background A key step in microbiome sequencing analysis is read assignment to taxonomic units. …

What kind of DNA lingers on ATM keypads? Your food, your skin microbes…and (maybe) parasites

Amidst the November/December holiday chaos, myself and co-authors were proud to witness the publication of a neat new paper focused on ATM keypads in New York City. Yes, just like all other surfaces in the Built Environment, those ATM keypads are harboring lots of microbes and bits of orphaned DNA! This ATM keypad study was work that …

Wanted – recommended service providers for microbial sequencing (genomes, rRNA, metagenomes, etc)

In January 2014 I wrote this post about “microbiome” sequencing services. I have gotten many outside requests for the following information — what places (companies, Universities, government agencies, etc) provide contract services for rRNA PCR and sequencing? Source: Request — Information on Places that do rRNA sequencing as a service — microBEnet: the microbiology of the …

Method of interest: precision sequencing of near full 16S rRNA genes on a MiSeq (from @Cath_B & @koadman)  

Definitely worth checking this one (from Burke and Darling) out if you do microbial diversity studies … Background The bacterial 16S rRNA gene has historically been used in defining bacterial taxonomy and phylogeny. However, there are currently no high-throughput methods to sequence full-length 16S rRNA genes present in a sample with precision. Results We describe …

New paper of interest on “Phylotags” – High-resolution phylogenetic microbial community profiling

This seems like it could be of interest to microbial community researchers: The ISME Journal – High-resolution phylogenetic microbial community profiling Abstract (with bolding by me) Over the past decade, high-throughput short-read 16S rRNA gene amplicon sequencing has eclipsed clone-dependent long-read Sanger sequencing for microbial community profiling. The transition to new technologies has provided more …

Wrap up of talk by Norm Pace on “Metagenomics and the Tree of Life”

Norm Pace gave a talk at UC Davis yesterday on “Metagenomics and the Tree of Life”. I and a few other people posted live Tweets from the talk which I have compiled together via the Storify system.  This “Storify” is embedded below. In addition, Lisa Cohen, who was at the talk posted her notes which …