Of possible interest to studies of microbiology of the built environment is a new paper: PLOS Pathogens: Asthma and the Diversity of Fungal Spores in Air. By Anne Pringle from Harvard University, the goal is summed up pretty well by the author
With this primer, my aim is to facilitate communication by providing doctors with a basic, modern guide to spores, by teaching mycologists the essential facts of asthma, and by providing patients with a succinct summary of what is known about spores and asthma. By highlighting the use of emerging metagenomics technologies in ecology, I intend to illustrate how these tools might be used to more thoroughly understand the potential diversity of fungi involved in asthma.
It is pretty brief but has some comments and discussions of interest to the studies of microbes in buildings.
RT @Dr_Bik: New at #microBEnet: New #PLOSPathogens paper: Asthma & the Diversity of Fungal Spores in Air: Of possible inte… http://t.co/8…
“While establishing a cause and effect between spores and
asthma may remain a challenge, metagenomic technologies will
establish correlations between the diversity of fungi and asthma
more effectively.”
The authors wrote: “While establishing a cause and effect between spores and asthma may remain a challenge, metagenomic technologies will establish correlations between the diversity of fungi and asthma more effectively.” This is an interesting prediction (hypothesis?) based on an assumption that the diversity of fungal species is somehow relevant to the associations or correlations between asthma and fungal exposure. It seems to me to rest on an unproven assumption. I did not see any evidence for this in the paper. But if there is evidence to support this, I hope someone will help readers find it.
The author seems to go on to contradict this assumption by writing about a single, neglected-but-possibly-important species: “Perhaps profiles of lungs will reveal basidiospores as more common than previously thought, or identify a currently undescribed species as particularly abundant.”
Hal, thanks for letting me know about your comment. I’m using the word diversity to imply that species are not equivalent; I’m not using diversity as a proxy for species richness. I think there are two possibilities, 1) all species are equivalent, and diversity doesn’t matter, so total counts of spores (regardless of species) will tell us what we need to know about spores and asthma or 2) species are not equivalent, and diversity does matter; some species’ spores will cause asthma, while others won’t. It _is_ a hypothesis, and I do think novel technologies will help us to explore it. I did not mean to imply that more species=more problems, tho that’s an interesting idea. I hope that’s a useful clarification, Anne
“Diversity” is a term we need to do a better job of defining in context. It has many many uses, even within the microbial ecology world.
Sometimes it means the number of species in a sample. This is also known as alpha diversity.
Sometimes it is used to refer to an alternative measure of alpha diversity which includes information on the relatedness of the species in the sample. This is usually measured from a phylogenetic tree and is referred to as phylogenetic diversity or sometimes phylogenetic alpha diversity.
Then there is beta diversity which is a measure of the diversity between samples. It too can be measured from species lists or from phylogenetic trees.
Then of course there is functional or trait diversity, which could be different from species or phylogenetic diversity. Functional diversity can also be measured within and between samples and it cane be measured in list – based approaches and in phylogenetic tree based approaches.
Then there is within species diversity – usually measured by some type of population genetics or population genomics.
I could go on and on and on. “Diversity” is way to general a term for many discussions.
Thanks to Anne and Jonathan for their comments.
I have often been puzzled as to how to interpret the reported results of microbial ecology research when the term “diversity” is used to characterize the results of one or more of the types of analyses that Jonathan described. I wonder if there isn’t some way to encourage more specificity in the reporting.