The coffee-machine bacteriome

bacteriaFrom a new paper in Nature, Scientific Reports:

Microbial communities are ubiquitous in both natural and artificial environments. However, microbial diversity is usually reduced under strong selection pressures, such as those present in habitats rich in recalcitrant or toxic compounds displaying antimicrobial properties. Caffeine is a natural alkaloid present in coffee, tea and soft drinks with well-known antibacterial properties. Here we present the first systematic analysis of coffee machine-associated bacteria. We sampled the coffee waste reservoir of ten different Nespresso machines and conducted a dynamic monitoring of the colonization process in a new machine. Our results reveal the existence of a varied bacterial community in all the machines sampled, and a rapid colonisation process of the coffee leach. The community developed from a pioneering pool of enterobacteria and other opportunistic taxa to a mature but still highly variable microbiome rich in coffee-adapted bacteria. The bacterial communities described here, for the first time, are potential drivers of biotechnologically relevant processes including decaffeination and bioremediation.

The authors note:

The presence of bacterial genera with pathogenic properties and the fast recovery of the communities after rinsing the capsule container, strongly suggest the need for frequent maintenance of the capsule container of these machines.

In related news from a few years ago, scientists in the US have genetically modified an E.coli strain so that it is ‘addicted’ to caffeine. Yes, but will E. coli prove theorems?

Hat tip: Paul Kedrosky.


While this article is mostly just fun, the microbiome is the new frontier. Well, that is fun too, with impacts on everything from weight loss to dreams of off-world colonies.

It will be an interesting 20 years as the science matures.

Takeaway: only consume coffee brewed in the home?

I'd take SBUX's cleaning regimen over the typical home or office by a mile.

I'll take my cleaning regimen over SBUX's: while cleaning, like cognition itself, is only ever an approximate enterprise, I have persuaded myself I vastly prefer my own coffee-making and coffee-serving.

Clean the capsule container ? How ? By breaking my Nespresso ?

I know not the first thing about Nespresso brewing: my humble coffee brewing apparatus is a Krups model, for which I use disposable Melita non-chlorinated filters, into which I put various non-SBUX coffees and Brita-filtered water. (I'm not dead yet, or if I am, no one's had the decency to inform me.)

Edward Burke - I understand - I've got a cheapo Nespresso that hasn't killed me in 5 years - only reasonable means I can see to clean it would be trashing it (I'm assuming the standard "run descaling solution through it" isn't enough). Ah well. What does not kill me give me the jitters,

I buy green coffee beans and roast them in an antique hand-cranked drum roaster over my gas stovetop. Having roasted hundreds of pounds of coffee this way, I like to think I know something about making coffee.

I brew my coffee in a very primitive apparatus. There are native people in Ethiopia that would consider my method primitive. It's a repurposed pickle jar that I secure a paper coffee filter over with a rubber band. I boil water over the stovetop, cool it by passing three times between the pot and a ceramic bowl, pour it over ground coffee in my cup, give it a stir, then filter into the pickle jar. I rinse the cup, then pour the filtered coffee into the cup. I'm very satisfied with my coffee, and everything gets cleaned or replaced before being used again.

Nespresso? What's that? Is it like a Keurig? Preground coffee is only one step up from instant coffee. I don't hold ground coffee for more than 30 minutes, and I don't hold roasted beans for more than a week. (Roasted beans need to age for 2-3 days minimum for maximum flavor, then they're good for maybe another week -- I don't know exactly how long because they always get used sooner than that.)

Yes, because one can always count on the conscientiousness of angry Liberal Arts majors who feel the work is beneath them and the other has conspired to deny them their rightful place as credentialed but unskilled labor.

Where do people live that Starbucks baristas actually fit this description? I mean, independent coffee shops, maybe, but Starbucks?

Don't worry until someone finds pathogens (or toxins) in the coffee itself.

A simple cone filter is easily cleaned, and takes water hot from the kettle (hotter than most makers).

Of course grinders ...

Electric kettles are terrible here in 110V land.

I live in natural gas land, use a real kettle.

Maybe you need a kettle with a battery built into the base to bring it up to 2,400 watt territory or higher? Sure, building a heat exchanger into it would be more efficient, but the initial capital cost might be a bit high there.

Between the fairly rapid discharge requirements, weight and volume limitations, and the need for many duty cycles I don't think the necessary battery technology exists.

Well, a supercapacitor might make a lot more sense than a battery, but it would have to be one with an extremely low self discharge rate otherwise it would end up being horribly energy inefficient. Batteries are also up to the task. They have come a long way and electric car battery packs are examples of batteries with high power, energy density, and lifespan. And given that people are happy to have have large and heavy coffee machines sitting on their benches weight and volume may not be a problem.

But that that's probably still way over designed. It would probably be much simpler and cheaper to have a kettle with a well insulated flask that keeps the water warm so it can be quickly brought to the boil. And then there's a kettle which just boils one cup's worth of water at a time. I've just read that an outlet in the US can output 1,800 watts which isn't bad, so to boil one cup of water would only take about 39 seconds. And kettles could have a camera a microphone and a clock and turn themselves on when they see and hear things they learn to associate with coffee making. The cost of the electronics required for that are pretty amazingly cheap these days.

Most houses have outlets with 15A @ 110V, but sometimes you see 20A instead. If you were renovating your kitchen you good put in an extra 220V outlet you might be able to use a European kettle with an adapter of some sort.

On a counter-germaphobe note, if your Mr. Coffee hasn't killed you yet, you're probably well adapted.

For me, French press.

Right. If you clean it you just give something else a chance to colonize your machine.

Communities are always at work solving the problems of the moment to ensure their kind perpetuate throughout time. They are very alert to changes in their environment. Humans should be so alert. Three theses I offer: 1) Community precedes cooperation; 2) Community is how life solves all problems; 3) Security is the primary purpose of community. All together this is the "community motive". It preceded the profit motive and enables that through civilization building. Coffee-machine bacterome are enabled by human built environment.

Well, yeah, rinsing the capsule container would reduce the concentration of antibacterial caffeine. Not to mention, the machines are apparently not brewing at the proper temperature (205 F). Also, no word mention on whether they controlled for the use of froo froo coffee pods that would have sweeteners and other flavorings to contaminate the coffee.

I wonder if you could promote bacteria colonies with beneficial properties, as in yogurt or kombucha? "New! A coffeemaker with bacteria that won't kill you! Be sure to wash only with lukewarm water!"

Let them drink tea.

"Caffeine is a natural alkaloid present in coffee, tea and soft drinks with well-known antibacterial properties. Here we present the first systematic analysis of coffee machine-associated bacteria" [SNIP]

What a simplistic 'tee-up'.

1) There are thousands of flavinoids, alkaloids, phenols, etc in coffee. Its an extremely complex natural product.

2) Why would anybody want to 'decaffeinate' coffee? That's like taking octane out of petrol!

Taking octane out of petrol makes it more efficient and more powerful. Adding octane only prevents knocking.

Yes, bacteria can prove theorems, via genetic algorithms.

Just because it has germs does not mean that it's a problem. We humans and our amazing immune systems evolved to work optimally in a world crawling with germs. Let's not assume that every de-germing is an improvement for human welfare.

+ 1

Not only this, but won't the researchers think about our [gut] micro biomes!

150 years ago the germ-theory of disease didn't exist . . . something to think about. 1945 you could walk down a city street and get TB by a passing pedestrian coughing. 100 years ago they'd 'blood let' you to take the bad sprits out of your system . . . We're all Steve McQueen in Papillion to some extent.

In the Mesozoic era, toasters ruled the earth.

@Mark Thorson,
" it by passing three times between the pot and a ceramic bowl"
What are you trying to achieve here? And how do you ensure that the beans you purchase are fresh and not eons old? I always worry about that, so have given up the grinding process for now in preference to a simple 14 year old Alimenti moka maker. Of course that means using ground coffee (Lavazza), which, I have to admit, doesn't come close to my best attempts at the grinding method.
Just don't get the fashion for these Nespresso type coffee makers. I can only presume it's laziness combined with ignorance of what decent coffee should taste like.

I have been using a Black/Decker auto coffee pot for about 50 years. Probably my 4th one
by now. My "on sale" cheap coffee tastes just fine. I am on my way to 90 years old and
haven't died from an OD of coffee yet. I clean it occasionaly with a vinegar perk. My
granddaughter and husband have some fancy thing that cooks one cup of coffee at a time.
I think its called a Kurig. Doesn't taste any different from mine. My pot does use a filter.
Just a 4 cup size. I have seen many inventions happen and changes up the gazoo,
but my coffee making stays the same. Ciao. R

P.S. If I were going to get sick and/or die from bad bacteria in coffee, don't you think it would
have happened by now???

There is one May MOAM left. I'll put your name in it, and could you please send me an email so I can keep my BotMo email files in order? Thanks!The eldmares are tiny little beads, but they're eldmares. (They're more to educate people on color than to make a big piece of jewelry with.)And I went overboard on flower and leaf beads. Again. ;-)

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