New article in the Microbiome Times

Defining the term “strain” is a conscientious issue within the microbiome field. Standards by which researchers classify strains are lacking, and the complex nature of microbiome samples makes developing defined methodologies for distinguishing strains difficult.

In an article for the Microbiome Times, our CSO Bjørn Nielsen shares how the term “strains” actually refers to clonal populations, and explains which methods can be used to differentiate bacterial strains in microbiome research.

What are some common methods used to differentiate bacterial strains in microbiome research?

“The term “strain” has, in the microbiome era, drifted away from its original meaning of an isolate that had been “strained” on a growth medium. It now refers to a clonal population, including those found in our microbiomes. In my view, we should consider strains as clonal populations with a very recent common ancestor, using the phylogenetic relatedness of the strains as a framework for understanding them. This can be done using single-nucleotide polymorphism and maximum likelihood methods to estimate phylogenetic relatedness at this level. Organizing the strains in a phylogenetic tree allows us to correlate traits or phenotypes with the evolution of the strains. This helps us understand how clades are associated with the human host’s clinical conditions or responses to treatment. Furthermore, we can place isolated strains in the tree with the strains we observe in microbiome samples. In doing so, we can link information from human studies with isolated strains and vice versa, and perhaps discover new applications areas for strains.

My key message is that strains are unique, and since we cannot generalize something unique, it does not make sense to think of strain-level as a taxonomic level. We need to understand diversity at this level de novo and use phylogeny to generalize and learn about their traits.”

Read the full article here.

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