Microbiome on a chip

19 May 2019

Interview with 

Don Ingber, Wyss Institute at Harvard University

BACTEROIDES-FRAGILIS

Microscope images on bacteria on a slide

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Some people call it “the organ we overlooked”, and it’s surprising that we did, given that it weighs as much as your liver, and contains more cells - and about 20 times as many genes - as the whole of the rest of the human body put together. But the importance of the “microbiome” - the community of trillions of microbes that live on us and in us - is now beginning to be appreciated. The outstanding problem, though, is that the role it plays in the body in health and disease is very hard to study, because the conditions that support the hundreds of different strains of microbes that live in contact with our own cells are tricky to recreate. Chris Smith spoke to Harvard’s Don Ingber, whose team has developed a way to reproduce the microbiome, alongside human intestinal cells, in long-term culture, which has just been published in Nature Biomedical Engineering…

Don - I've been in medicine for many years and one of the biggest paradigm shifts I've seen over the last 10 years is the discovery that the gut microbiome, the normal microbes that live in our intestines, play a fundamental role in health and disease, and there's really no way to study how they interact with the living cells in our intestine in a simple way. Everything we know about it is based on genetic analysis which is essentially guilt by association. This bug is there or that bug is not there in people with different problems or healthy states, but it doesn't show causality.

Chris - Why is it difficult then to study how the relationship evolves between host i.e. us and microbe?

Don - We don't think about it, but in the centre of our intestine (the lumin), oxygen levels are extremely low and so there are microbes that live in that environment that actually die at higher oxygen levels, whereas our cells they need oxygen. And in the body there's a gradient of oxygen meaning it's high in the blood vessel and it gets lower and lower as you get further towards the centre of the space of the intestine. And bugs of different types survive in these different regions, so we had to figure out a way to make all that happen by basically mimicking the way it works in our body.

Chris - How are you doing this? Is this in a dish?

Don - It's in a device we call a "human organ on a chip". These are the size of a computer memory stick, they have two hollow channels less than a millimetre wide right next to each other, two centimetres in length. The wall between them is porous meaning things can go back and forth. We literally isolate cells from biopsies from the intestine of human patients and we culture them on one side of the porous membrane in the first channel. The opposite side we have blood vessel cells that line the small vessels, capillary blood vessels in our body. By flowing oxygenated fluid or medium through the blood vessel channel we get a gradient very much like in our bodies, so that is enough oxygen for the capillary blood vessels cells and intestinal cells to survive. But the oxygen gets so low in the middle of the space above the intestinal cells that we can get all types of bacteria to grow, ones that grow in low oxygen, mid-level oxygen and higher.

Chris - Essentially then, the oxygen is being delivered by the channel that we're pretending is the blood flow?

Don - Exactly like in our body, yes.

Chris - And it's moving across that porous interface between the two channels.It sees the intestinal cells first so they get first dibs at the oxygen, some will then make its way into what we are pretending is the inside of the bowel, and that's where you've then got the bacteria growing?

Don - Exactly right. And interestingly, the human intestinal cell spontaneously form these fingerlike structures called villi that increase the absorptive surface area of the intestine. And they also put out mucus and that mucus is a very important boundary between the cells in your gut and the bacteria and it really is an important part of how they live and grow in our intestine. It's really quite an amazing mimic of how our body is built and how it works.

Chris - How do you get the bacteria in and where did they come from?

Don - We get bacteria from stool specimens from neonates in the neonatal intensive care unit of our Children's Hospital here in Boston. And there are hundreds of different microbes there but we’re able to keep hundreds of different microbes alive in direct contact with these human cells. That really is a first.

Chris - And what is this going to enable us to do - now you've got this model system working - that we couldn't before?

Don - We're funded by the Gates Foundation to study malnutrition in children in the Third World. And there's communities of microbes that actually contribute to the intestinal injury which is characterised by loss of those fingerlike extensions, so less area to absorb nutrients and a breakdown in the barrier which actually causes inflammation and injury. We could mimic that by culturing multiple microbes on these chips under similar sort of hypoxia, low oxygen conditions that mimic our intestine.

Chris - And what about when we give people doses of antibiotics because that's the other issue at the moment isn't it? We are very worried about antibiotic resistance but also the knock-on effects through life, especially when you encounter antibiotics at a very young age. Will your system enable us to ask, if I do this, what does it do to the community of microbes that live in the intestine?

Don - It's absolutely true that if you take antibiotics as a child you can have a long-standing impact on the microbiome, and that is precisely the type of experiment we can carry out. You could look at probiotics people take and see whether they in fact do work, and we're doing all these types of experiments now...

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