Sara Di Rienzi, Cornell
Listen Now Download as mp3 from the show eLife Episode 5: Human Sperm, Gut Bugs and Decomposition
Meet a newly-described bacterial family known as melainabacteria, which had previously been written off as cyanobacteria until Sara Di Rienzi came along...
Sara - It’s been known for a while, that within the human gut there are sequences that appear to be very closely related to cyanobacteria. So closely related that they’re generally just assumed to actually belong to cyanobacteria. So, whenever these sequences pop up, they just automatically are assigned as cyanobacteria when they’re not. And where this really gets confusing is that cyanobacteria are photosynthetic, so they like to be in places where there’s light. That’s how they live, that’s how they get their energy.
Chris - And where you’re looking, naturally the sun doesn’t shine terribly often.
Sara - Exactly, there’s no light in the human gut.
Chris - Well not on a good day anyway.
Sara - Yeah, exactly. So, when most people read, “Oh, cyanobacteria in the human gut,” they say to themselves, that must be the plants we’ve been eating. It must be from the photosynthetic cells that are contained within plants and not that this is some cyanobacteria that’s actually growing in the human gut. So, what we were setting out to do is to try to actually determine, well, what exactly are these bacteria? And our lab has tried for some time to actually grow them in the lab and this has proved to be very difficult and unsuccessful. What we did was complete sequencing of faecal samples. I worked specially in collaboration with Itai Sharon, who’s a post-doc in Jill Banfield’s lab. And they have this really amazing technique which allows them to sift through a pool of DNA sequences and figure out who belongs to who. So, what the method expects is that DNA that comes from one organism should all be in about the same amount, whereas DNA that comes from another organism should be in a completely different amount.
Chris - I get it, and so you can begin to assemble the bits of DNA that go together based on the frequency of those components. What did that tell you?
Sara - So, what that allowed us to do is to get all the DNA that belonged to this weird cyanobacteria light organism all together, and then from there, we could go and use traditional characterisation of genomes based on information we’ve learned by studying thousands of other bacteria over the years.
Chris - And then it became patently clear this was not a cyanobacteria and this was something else?
Sara - Yes. First, we firmly established that this is absolutely not a cyanobacteria.
Chris - So, what actually is it, and what does it do, and why is it there?
Sara - So, we’ve termed this new group of bacteria, melainabacteria, and we’ve discovered that it’s entirely non-photosynthetic. So, it’s very different metabolically from cyanobacteria, and instead it’s entirely anaerobic and it uses fermentation to get its energy. So, that means it’s breaking down sugars.
Chris - But given its stark differences to cyanobacteria, why is it that at the same time so similar to them?
Sara - Right. So, there’s a specific gene, the 16S ribosome, this is the best marker we have to understand evolution. And so, by following that, we see that it is closely related to cyanobacteria. So, what we hypothesise is that at one point there was a general ancestor, and that then it either went off into the light, so to speak, and figured out how to use light for energy, or it ended up burying itself in dark places like the human gut. In those environments, it had to just rely on fermentation entirely.
Chris - So, if we look outside the human gut, where else would we find this organism, this family, and what sorts of things does it do in the environment or in other environments other than in us?
Sara - So it’s also found in water systems. We specifically were able to sequence one out of an aquifer. What exactly it does, we’re not 100% certain of. We have some ideas of what it does in the human gut. We’re assuming metabolic similarities to a group of organisms called, firmicutes. So, firmicutes act as major fermenters in the large intestine where they break down sugars and can convert them to short chain fatty acids, and we think these melainabacteria can carry out a similar process.
Chris - So, any evidence that they may be linked to pathology, or are they thought to be just passengers that are harmless.
Sara - Yeah. We think they’re actually if anything, beneficial. They’re also able to produce the B and K vitamins which the host does need to get from its gut bacteria, and there’s some evidence, based on its interactions with the immune system, that it would not be a pathogen.
Chris - So, what questions now remain outstanding? You’ve found this organism. You’ve proved what people have missed all along, but now, what are you going to do?
Sara - Oh. We’d love to know what it looks like. We haven’t seen what a cell of it looks like, yet.
Chris - So, apart from trying to grow it and look at it so you can have pretty pictures of it, and publish the first EM of whatever this is, what else are the big questions you’re going to ask of it genetically and evolutionarily speaking?
Sara - So, we’d like to get a better idea of why it’s enriched in herbivores, for instance. Some of our findings is that it’s enriched in mammals that are herbivores.
Chris - Does that include human vegetarians?
Sara - Unfortunately, there’s not enough data for us to be able to really answer that question. However, we were able to compare humans living in more western cultures versus those in Venezuela and in Africa, and we found that they are more present in the people from South America and from Africa, which are also on more vegetarian diets. But we don’t have that 100%, “Yes. If you eat your vegetables, you’ll end up with melainabacteria in you.”