You Will Not Be Using a Handheld DNA Sequencer to Characterize the Microorganisms In Your Kitchen Anytime Soon

And Why On Earth Would You* Want To?

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A non production version showing the sequencing device fitting in the palm of a hand.

Perhaps you might have heard about the MinIONn DNA sequencer from Oxford Nanopore technologies. This palm of hand sized device has been all the rage in the molecular/micro biology community for the past five to ten years and is now breaking through into the mainstream consciousness of the average American consumer. Mostly this is due to a relentless marketing onslaught accompanied by wave after wave of media fawning and hyperriffic bloviating. The company is pushing the idea of the average American using one of these devices to sequence the bacterial microbiome of their kitchen (as one example) and in so doing obtain the identity and relative proportions of said population. With this information in hand the consumer can then……??

There are a host of technical problems/concerns/considerations related to sampling a kitchen environment in a way that could (in theory at least) generate some useful data (useful for government or industry research microbiologists and possibly epidemiologists) but the company has shown no interest in explaining the complexities of what they are proposing. The purpose of this article is not to dissect the technical issues (which are significant) but instead to focus on the practical applications of the information. Assuming, for the sake of argument the technical details can be worked out (for the record I don’t believe they can, at least not in a way usable by the average American consumer) what exactly would such a person do with that kind of information?

For those with high school aged children it would be a Godsend as they could, if they were so inclined, hand their children a virtually guaranteed A on their science project for biology class, but what about for everyone else. The user of this test would would most likely receive some sort of report in the form of a pie chart or bar graph that looks a lot like the figure below.

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An example microbiome data plot. This is a real world example in which the relative proportions of the bacteria present in an enrichment are measured at the beginning and end of the enrichment period. This is not representative of a kitchen in any way though this is a food sample enrichment.

I am a working research microbiologist with 15+ years in various research roles in government and industry and even I have no idea what the “Glutamicibacter protophormiae group” consists of or it’s significance to human health or anything else.

Of course I have the knowledge and resources available to quickly find out but I can only imagine what the average consumer would take away from something like this, and their microbiological resources are limited to what they can find with a Google search and Wikipedia. In case you were wondering the screenshot below is what you get when you do those searches.

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Google and Wikiepedia search results

Not a lot of help there as you can see. Most consumers who have the money to purchase something like this would be smart enough to insist that the money they are spending result in some benefit for them and/or their families. A better understanding of the taxonomy of the bacterial population of their kitchen counter top while fascinating to some (myself included) is not going to motivate many/any ‘regular’ people to fork out the kind of money a test like this is likely to cost. As to what that cost will ultimately be it is very difficult to say. I have yet to pay for a microbiome analysis myself but I have been told that one can be had for <$100 with results in less than 1 week, and also told it will cost around $2000 and I will have results in 4–6 weeks. The details of why these big discrepancies exist are not relevant to this discussions but suffice to say the prices and turn around times vary considerably. In general the cost of sequencing has been rapidly decreasing and turn around times for analysis have gotten much faster. (I am leaving out the problem of the back end analysis of the data which is an even bigger issue in terms of TATs. Bioinformatics analysis is not fast and even if sequencing could be done instantaneously the data would be of little use until it could be processed by an expert bioinformaticist with sophisticated analysis software. Those pretty pie and bar charts don’t generate themselves and suffice to say excel is not going to get it done). That said, the cost is still out of the range of your average consumer and the current TATs are not nearly fast enough to give any information that could be useful in the kitchen scenario I have been describing. Microbial populations change considerably with time, especially in as an environment as dynamic as a kitchen. Without real time or same day results any information you would get would be to dated to allow any decisions that could be of any known or predicted consequence.

*unless you happen to be a microbiologist, epidemiologist, or high school biology student

Written by

Research scientist (Ph.D. micro/mol biology), Thought middle manager, Everyday junglist, Selecta (Ret.), Boulderer, Cat lover, Fish hater

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