Nice step by step instructions on metagenomic sequencing from air samples – only one problem – it is Closed Access

There is an interesting and potentially very useful paper just out:

Optimized DNA extraction and metagenomic sequencing of airborne microbial communities

A brief summary from the journal:

This protocol enables collection of airborne particulate matter; and after sample pretreatment, it allows sufficient quantities of microbial DNA to be extracted and prepared for downstream applications such as metagenomic sequencing.

And the abstract:

Metagenomic sequencing has been widely used for the study of microbial communities from various environments such as soil, ocean, sediment and fresh water. nonetheless, metagenomic sequencing of microbial communities in the air remains technically challenging, partly owing to the limited mass of collectable atmospheric particulate matter and the low biological content it contains. Here we present an optimized protocol for extracting up to tens of nanograms of airborne microbial genomic Dna from collected particulate matter. With an improved sequencing library preparation protocol, this quantity is sufficient for downstream applications, such as metagenomic sequencing for sampling various genes from the airborne microbial community. the described protocol takes ~12 h of bench time over 2—3 d, and it can be performed with standard molecular biology equipment in the laboratory. a modified version of this protocol may also be used for genomic Dna extraction from other environmental samples of limited mass or low biological content.

The paper has a detailed step by step instruction guide for doing the work.  Really really detailed. Sounds pretty cool right?  And possibly very useful to people working on airborne microbes.

The only problem – and it is a big one to me – it is a Closed Access paper and it is in a journal that not so many subscribe to – Nature Protocols.

I am going to contact the authors to see if I can get them to post a copy of the paper or a preprint somewhere in the hopes that that will allow everyone access to it.



One thought on “Nice step by step instructions on metagenomic sequencing from air samples – only one problem – it is Closed Access

  1. I appreciate the authors attempt at developing a protocol for metagenomic analysis of air samples. The authors are correct that metagenomics of air samples is incredibly challenging, mainly due to the extremely low biomass. With that said, I have some concerns about the protocol and relevance of this methods paper.

    First, I was not sure why particles suspended in buffer were filtered through a 0.2um filter, this seems like it will remove all the bacterial particles and some of the viruses (see previous post discussing difference of filtering air vs. liquid.) Upon further reading, I realized they actually extracted particles directly from the 0.2um filter, meaning they lost a large bulk of viruses (those less than 200 nm) for metagenomic analysis, which seems problematic (and maybe the reason they were unable to get enough RNA?)

    Second, I am not sure how “effective” the reported method is compared to much simpler methods (i.e. extracting DNA/RNA directly from the filter.) In table 1 the authors report 50 ul of genomic material at concentrations ranging from 0.073-.632 ng/ul. Other studies that have simply extracted genomic material directly from the filter have similar concentrations, with less steps and places to introduce contamination.

    Perhaps, I misunderstood something and if anybody else has insight please feel free to share and/or correct me.

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Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. My lab is in the UC Davis Genome Center and I hold appointments in the Department of Medical Microbiology and Immunology in the School of Medicine and the Department of Evolution and Ecology in the College of Biological Sciences. My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis (see my lab site here which has more information on lab activities).  In addition to research, I am heavily involved in the Open Access publishing and Open Science movements.