What microbes actually grow on your food?

And can Illumina identify food just by its microbes?
07 June 2024

Interview with 

Trevor Ho, Illumina




I don't really know how you got in here, but welcome to my kitchen. I suppose you just caught me in the middle of preparing a delicious and very healthy meal that purely coincidentally you cannot see. Now, whilst I love preparing my fresh, very fresh and so healthy meals, let's be honest, there comes a time when the leftovers, the food that has been out for a couple of days on the side, maybe look a bit tempting. We're busy people and a fair few of us were all students once. We don't talk about what happened back then. These things can happen. And let's be honest, until you see the white puffs of disgusting random fungi emerge on the food, surely it's fair game, right? I mean, how bad for you can it really be? What really grows on your food? Now this to me is a particularly interesting question, but one that has immaculate timing because genetic sequencing company Illumina, has just handed me far more power than anyone man should ever have. I have in my possession five samples of everyday household food, food that you and I would use in any meal without thinking, except I've left them out for two to three days to see what might grow on them. I'm now going to take those samples over to Illumina and see what exactly is growing on my food. But there is a slight twist.

Will - Here's the thing. I could very easily take a bag full of swabs of old food to Illumina and ask, 'Hey, what's growing on this?' And that would be no problem at all for them to answer, but I don't think that's flexing their muscles enough, so I'm just not going to tell them what the food is. And so the question becomes twofold. One, what is growing on my food? But two, can they use their best detective intuition to work out what the food was purely based on what was growing on it. Now that sounds like more of a challenge to me. Now, if you'll excuse me, I have to go hand a bag of old food to a complete stranger.

Trevor - Hello Will, my name's Trevor. I work here at Illumina as a senior scientist. So yeah, I'm happy to grab your samples, which you're ready for me to try and sequence.

Will - Lovely. I have this bag full of rotting food. No one has ever been happy to take this from me before, but I do hope you can make something of it.

Trevor - Thanks very much. I see like a couple of tubes in front of me. I'll grab them into the lab and then I'll try and take some of the material out and then see where I can sequence them. Thank you.

Will - The bag of detritus has been successfully left at Illumina and they've asked for a couple of weeks to sequence it and see what they can find. But I'm going to give them four seconds. Okay. Let's see how they did.

Will - Now that you've received my mystery bag of strange samples of food, could you talk our audience through what sequencing you did on them?

Trevor - Sure. In general, the sequencing that we apply to those samples is called 16S sequencing, and basically 16S is often described as a housekeeping gene. Every bacteria must have one of them. But the interesting thing is that as bacteria evolve into different species, there are minute differences that accumulate on this housekeeping component of their genome over time. So by reading information from this 16S region or just like a really important essential region, then we're able to tease apart which bacteria it is. You can imagine as every bacteria have a signature region within this part of the genome. The kind of library prep or the sample prep that we apply to them is basically making copies and copies and copies of this very essential region so that we can read them accurately and with high level of confidence.

Will - You did all this and you found some interesting looking bacterial microorganisms. Was that the only tests you did?

Trevor - I'm glad I bring up Will. Actually no. So I just mentioned that we try to study the bacterial population by 16S sequencing. We actually have a very similar technology that tries to look for the fungi population, and that's called ITS sequencing. It's the same concept as before, copy paste. There's a region across all fungi that are just pretty much consistent, but surprisingly we didn't really find any. So across all the five samples, we could not identify fungi from those things. I guess that is an indication that maybe just for only three days, it's not sufficient for fungi to cause the food service and become the major source of infection. But that's also part of the reason why I was able to rule out white bread because I would've expected mould to grow on it and that I'll be able to get something out of it. But that didn't happen.

Will - Given that, you know, this food sample was prepared in perhaps not the most sterile environment being my kitchen. What were you able to tease apart from the microorganisms growing on these samples?

Trevor - So it's quite clear that the bacteria that are growing on food samples that you gave me are very diverse and probably some of them are things that we've never seen before. So it's really hard to pinpoint what's exactly in there. We can only have some glance of information from the species that we can actually identify and in fact that weren't that many that we can do. But one thing that struck me is there is one species of bacteria called Acinetobacter Johnsonii, that is very prevalent across all the five samples I received. And when I look up like when I Google and try to figure out, okay, what is this like, um, bacterial species, it lives everywhere. It lives in the sea, it lives on the soil. It is even reported to be isolated from human skins. So it's very difficult for me to guess where that bacteria actually comes from. Does it come from your hands or does it come from the air that is just floating around and then somehow sticks in the food and then they grow and then they colonise their food surface? I am not entirely sure. But what I do suspect is that that bacteria likely comes from processing because it is present in all the five swabs that you gave me.

Will - It's quite interesting though that I might have discovered a new species of bacteria in my disgusting kitchen. I mean my very sterile and clean kitchen. Yeah.

Trevor - Yeah but that also speaks to the truth of that, like, it's really important that we keep food hygiene, not just in the source of food, but rather in the processing, the cooking, the chopping and everything associated with it. There is good reason as to why people suggest actually different chopping boards for different food, to avoid cross contamination, that sort of stuff.

Will - No, absolutely. Iit more than highlights the delicate nature of having allergies as well, given how easy it's to cross contaminate in the same kitchen.

Trevor - Yeah, absolutely.

Will - So before we get onto the question of am I in any danger, obviously the samples I gave you were random samples of food and swabs of those. Could you do any detective work on them to work out what they might have been?

Trevor - I tried. I really tried, and I'm afraid I'm going to disappoint you. It's very difficult because as I said, like the majority of the population are things that we cannot identify, and then there is one single species that seems to dominate the rest. So from the rest of the population I have to make guesses based on something that looks strikingly similar. The one that stood out particularly is sample number three, which when I look at it has about 4-5% of Salmonella enterica. So salmonella is a bacteria, or a known possibly pathogenic bacteria, that can be found in paltry or other food or mostly meat. So I guess I'll make a guess that like sample three either belongs to uncooked raw beef or processed chicken. So that would be my guess. And then the other two samples, which I think I can make a bit more guess about, are sample one and sample two. These two samples, once I remove the unknowns and also like the dominating species bacteria, what's left behind are a bit of Pseudomonas, which would suggest to me that they come from something that has been in contact with soil because like that is where a lot of Pseudomonas bacteria live. So I think they are potatoes and also onions. Sample four and sample five are samples that contain, again, some salmonella, a bit of capsular oxytoca. Also these two are known pathogens, but also a bit of pseudomonas. But this is where I find it really difficult to guess what they could be. So that's my attempt and I guess like you can now tell me whether any of my guesses would land any hits.

Will - Well, I must say I'm tremendously impressed. Sample three was indeed chicken one and two are potato and onion. Yeah. And sample four was the aubergine. So you have done incredibly well there.

Trevor - Oh, so did I get three out of five? Correct. Amazing. I did not expect that.

Will - Absolutely stellar work. That is brilliant. All of that taken from one swab and some detective work.

Trevor - I was going in pretty much blind and not having a lot of confidence in anything that I can get all. So I'm amazed as well. I didn't know that there's that remaining few percent of the bacterial population that can tell me or can get me so close to the correct answer. I was really like just going blind.

Will - And the big question, should I be worried, was there anything on my food that was left out for maybe three days that I should not be ingesting?

Trevor - Absolutely. I think the general answer is yes, we should definitely be worried about, and there are two reasons. The first one is yes, we did find bacterial species which are known to be pathogens. So I mentioned Klebsiella, I also mentioned salmonella. So these two are things that could make people really sick if they get ingested. But at the same time there are also a large number of other bacteria, which they're not known to be pathogenic, but we don't know whether they are or not. But the very fact that if I eat expired food with so much bacteria that itself can upset your stomach, your guts leading to diarrhoea or general sickness or even vomiting. A lot of things consist of it. So I think in general, absolutely yes, it's not a great idea to eat food that has been left exposed to bacterial growth for a long time. And especially for people who are potentially in the compromise or they are not so good at contracting bacterial infection, getting ingesting this large amount of bacteria would pose a tremendous danger to them as well.

Will - So it comes as kind of not a surprise at all, but also a terrifying revelation that leaving food out for not actually that long in the grand scheme of things can accumulate some really nasty stuff on it.

Trevor - Yeah, really I think the best advice is to maintain good hygiene and try to consume foods that are cooked and ready to eat.


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