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Caffeine-Resistant Bacteria

January 7, 2016

The industrial revolution was fueled by coal, but our information age is fueled by coffee. We drink so much coffee that environmental caffeine is a good indicator of human presence. As the earliest riser in our research group, it was my responsibility to make the first pot of the morning. I was happy to do this, since I took more care in cleaning and brewing than most others, perhaps because of my many years of working in a materials laboratory. I also got to drink my coffee while it was still fresh.

During one of my visits to Bell Labs in the 1970s, I was treated to one research group's coffee. They had taken a scientific approach to the problem of keeping coffee fresh on the hot plate by reasoning that stale coffee was caused by oxidation. As a consequence, they flowed nitrogen gas, a convenient laboratory utility, into the open pot to displace the oxygen. As I remember, this process worked well.

A cup of coffee

A nice cup of coffee.

Since a cup's volume is defined as 8 ounces, serious coffee drinkers will opt for a 12 ounce, or a 16 ounce, mug.

(Wikimedia Commons image.)

In the 1980s, as research laboratories became more safety conscious, lab-brewed coffee was prohibited for some very obvious reasons, and we were forced to use the same coffee stations as our non-scientist colleagues. Eventually, those drip-style coffeemakers gave way to the single-serving types that are now common. As a coffee connoisseur, I've always preferred coffee made using vacuum coffee makers, or the Chemex process.

Chemex coffee, preferred by such "manly men" as Don Draper and James Bond, was the invention of the German chemist, Peter Schlumbohm. The Chemex process is essentially a drip coffee process using a thicker filter paper than others. The Chemex coffee pot has its conical filter holder and coffee pot integrated as one piece of glass. At one time I used a variant process that utilized a large plastic funnel and a standard pot. Now I use a Bunn, which is a step up from the typical coffeemaker.

Figs. 1 and 3 from US Patent No. 2,241,368, 'Filtering Device,' by Peter Schlumbohm, May 6, 1941

The Chemex Coffeemaker.

Figs. 1 and 3 from US Patent No. 2,241,368, "Filtering Device," by Peter Schlumbohm, May 6, 1941.

(Via Google Patents.[1]

Our corporate coffeemaker was generally clean due to my efforts, but most others are not. Biologists at the University of Valencia (Universitat de València, Valencia, Spain) have published a study on the bacteria they found populating the coffee waste reservoirs of ten different pod-type coffeemakers, and they also monitored the bacterial colonization process in a new coffeemaker.[2-4]

The research team sequenced the ribosomal RNA of the residue, and they were able to identify 59 bacterial genera with abundance greater than 0.01%.[3] This is a surprising result, since caffeine (1,3,7-trimethylxanthine), a natural alkaloid present in coffee, has antibacterial properties.[2] As a control check, they detected no cultivable microorganisms or bacterial DNA in the coffee itself, so the bacteria must have originated from the environment and grew under the warm and moist conditions present in the coffeemaker.[2]

Scanning electron micrograph of coffee machine bacteria

Scanning electron micrograph of coffeemaker bacteria after 21 days of operation.

(Fig. 4D of ref. 2, published under a Creative Commons Attribution 4.0 International License.[2]

In examining the temporal progression of bacterial species, there appeared to be a succession from generalist bacteria to bacteria apparently adapted to the coffeemaker environment.[2,4] This final bacterial pool is consistent with the bacteria types normally associated with the coffee plant and its subsequent processing.[2] In particular, Pseudomonas bacteria, a known caffeine-degrading bacterium was found.[2,4]

Bacterial colonisation in a brand new Nespresso Krups Inissia machine

Bacterial colonization in a brand new Nespresso Krups Inissia machine. The ecological succession of some bacterial taxa is shown by their relative frequencies.

(Portion of fig. 2B of ref. 2, published under a Creative Commons Attribution 4.0 International License.[2]

The authors advise that only careful cleaning of coffeemakers with bacteriostatic compounds, and avoiding contact of the drip waste with other parts of the coffeemaker, will prevent possible contamination of your beverage.[2] There might be a positive side to all this. Such bacteria might be effective in decaffeination without the use of solvents, and for environmental clean-up of contaminated soil.[2,4]

Another biohazard of coffee has been discovered by other scientists at the University of Valencia. They detected mycotoxins in an analysis of a hundred commercial coffee brands sold in Spain by liquid chromatography tandem mass spectrometry (LC-MS/MS).[5] Mycotoxins are toxic chemicals produced by filamentous fungi, and coffee can be contaminated by mycotoxins. Interestingly, decaffeinated coffee had a higher incidence of mycotoxins than caffeinated.[5] You can worry more, or perhaps less, in the knowledge that mycotoxins are found in many other foods, including cereals, dried fruit, spices, wine, cocoa, and peanut butter.[5]


  1. Peter Schlumbohm, "Filtering Device," US Patent No. 2,241,368, May 6, 1941 (Via Google Patents).
  2. Cristina Vilanova, Alba Iglesias, and Manuel Porcar, "The coffee-machine bacteriome: biodiversity and colonisation of the wasted coffee tray leach," Scientific Reports, vol. 5, article no. 17163 (November 23, 2015), doi:10.1038/srep17163. This is an open access publication with a PDF file available here.
  3. Supplementary sequencing statistics for ref. 2.
  4. Matthew Braga, "Your Coffee Machine Is a Breeding Ground for Caffeine-Resistant Bacteria," Motherboard, November 26, 2015.
  5. Ana García-Moraleja, Guillermina Font, Jordi Mañes, and Emilia Ferrer, "Simultaneous determination of mycotoxin in commercial coffee," Food Control, vol. 57 (November, 2015), pp. 282-292.

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