Challenges and Opportunities of Airborne Metagenomics

There is a new #openaccess paper out that may be of interest to many working on microbes in the built envronment or microbes in air (indoors or outdoors): Challenges and Opportunities of Airborne Metagenomics by Behzad et al. in Gebome Biology and Evolution.  There are some useful things in this paper and some strange things but it is definitely worth taking a look at.  The authors outline five challenges to metagenomic studies of microbes in the air:

  1. low density of microorganisms in the air,
  2. efficient retrieval of microorganisms from the air,
  3. variability in airborne microbial community composition,
  4. the lack of standardized protocols and methodologies,
  5. DNA sequencing and bioinformatics-related challenges.

And then they discuss these in more detail. One thing I found somewhat strange is the lack of discussion of the issue that some of the DNA from air samples will be coming from living organisms and some of it from dead organisms.  Regardless, the paper has some nice ideas and an overview of many aspects of airborne microbial sampling for DNA studies.



8 thoughts on “Challenges and Opportunities of Airborne Metagenomics

  1. AJ Prussin, Kyle Bibby, and I published a similar review last year, “Challenges of studying viral aerosol metagenomics and communities in comparison with bacterial and fungal aerosols,” in FEM Microbiology Letters. It’s not open access, but I would be happy to send you a copy if you contact me.

  2. If you apply the ecological definition of “microbial community”, there are no airborne microbial communities in buildings, simply because building air is too dry to sustain a community – worth checking a 24-hours-running sauna :-). Indoor air spreads either dormant (propagules) or dead microbes, that’s all.

    1. What is your evidence that building air is too dry to sustain a community? There are microbes living in the Atacama desert and Dry Valleys of Antarctica. Seems like building air could be a pleasant vacation for some of those organisms.

      1. Those microbes living in such extreme habitats are highly adapted to retrieve enough humidity from the environment. As they are so specialized, they would never survive in buildings.

  3. Sorry, I could only read the abstracts I am aware of high radiation-tolerant microbes commonly growing in buildings. The common Hyphomycete genus Alternaria is a good example. Its RH growth requirement: over 80%. I also known that thermophiles grow in animal sheds, mainly in compost piles. That they can be found in school dust, at much lower levels though, only illustrates that school surfaces are sinks for these microbes, not sources. A lot of microbes showing up in buildings as spores, though viable, cannot grow in the building environment, unless it can be documented.

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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.