This Week in Microbiology

With Vincent Racaniello, Elio Schaechter, Michael Schmidt

Episode 176: Elio has lots of colanic acid

Aired 18 May 2018

TWiM 176: Elio has lots of colanic acid

VINCENT: This Week in Microbiology is brought to you by The American Society for Microbiology at


VINCENT: This is TWiM, This Week in Microbiology. Episode 176 on May 10th2018. I am Vincent Racaniello and you are listening to the podcast that explores unseen life on Earth. Joining me today from Small Things Considered, Elio Schaechter.

ELIO: Hello there!

VINCENT: You know, last time we recorded was your ninetieth birthday.

ELIO: It was.

VINCENT: Happy birthday!

ELIO: I’m a nonagenarian.

VINCENT: A nonagenarian! Happy birthday.

ELIO: Thank you very much.

VINCENT: Also joining us from Charleston, South Carolina, Michael Schmidt.

MICHAEL: Hello everyone.

VINCENT: How are you, Michael?

MICHAEL: I am well!

VINCENT: You getting ready to go to Atlanta?

MICHAEL: I am getting ready to go to Atlanta but before I go to Atlanta I am going to go to Clearwater Beach, Florida, where I have the pleasure of chairing the seventeenth workshop for teaching microbiology and immunology to medical students, a conference that was started by the micro chairs some thirty odd years ago.


MICHAEL: So I’ve been chairing this meeting on behalf of the AAMC group for the past, this will be the third time that I’m chairing this meeting and it meets every other year. It’s sort of like Q but for medical school.

VINCENT: So what is the key to teaching microbiology to medical students, Michael?

MICHAEL: It’s probably, well, the theme for this year’s meeting is winnowing the curriculum. What does a graduating medical student need to know about microbiology and immunology? And unlike the other disciplines, and I’ll probably get hate mail for this, you know anatomy really is not changing all that much whereas micro and immune is evolving at a great clip. You just have to look at the advances in medications that we are developing for cancers that are specifically targeted to checkpoints in the immune system.

ELIO: There’s no sense in teaching them anything.

MICHAEL: This is true.

ELIO: By the time they graduate it’s not going to be relevant.

MICHAEL: Well yeah, and the great debate this year is do we need to be teaching about selective and differential media in an era of MALDI/TOF?

VINCENT: That is a great question.

ELIO: The answer is no.

MICHAEL: Do they really need to know about—well, this is good but unfortunately, the people writing the questions for the national board examination are us. And unfortunately there are sticks in the mud who think we need to still be teaching medical students wet labs and all sorts of other things and it’s—there’s a lot of blood on the floor after some of these discussions.

ELIO: (laughter)

VINCENT: I’m sure.

MICHAEL: But it makes for a lively activity.

ELIO: By the way, I am all for having a wet lab.

VINCENT: Yeah. You want to have a MALDI/TOF in that wet lab.

MICHAEL: Yeah. I’d like to have a MALDI/TOF and I’d like for them to appreciate how to do a gram stain, especially from fluids like spinal fluid and really teaching them the finesse associated with it in concert with drawing that fluid so they really begin to appreciate the importance of specimens and specimen collection.

ELIO: Let us know how it went, will you?

MICHAEL: I will. Maybe we’ll have a little discussion about it at our next meeting when we get together in Atlanta, which will be shortly.

ELIO: That’d be good.

VINCENT: Gee, Atlanta is in the beginning of June, isn’t it?

MICHAEL: It’s coming quick!

VINCENT: Yeah. We have one more here in the studio and then Atlanta, that’s right. Alright, we will first tell you another unfortunate passing in microbiology. Last time we told you about Allan Campbell. This time Stanley Falkow has passed away. He is also from Stanford University, as was Allan Campbell, and Elio just noted before we started recording Charles Yanofsky passed away some time ago. He was also at Stanford. Did any of you know Stan Falkow?

ELIO: I did, I knew him pretty well in the sense that we would get together at the meetings and have a cup of coffee. That was the extent of it, but one of his first graduate students of his modern era of molecular pathogenesis was Al Fitzburg who joined my department. So indirectly I got to know Stan quite well. So let me say something about him. He is considered the father of molecular microbial pathogenesis. What this meant is that he started the idea of using genetics, using mutants, to determine what the virulence factors are for certain organisms. And he codified that by calling it the molecular copostulates. What is it that you have to do demonstrated a factor is a virulence factor.

He, in the process, he trained an innumerable amount of people. The field is rife with Falkow alumni. They are all over the place and they all learned from the master that you can make things rather straightforward and simple in the world by answering that question. And he was a good guy, he had a wonderfully foul mouth, so it was fun to listen to him talk, and a very friendly, very warm person, I would say.

VINCENT: How about you Michael, did you know him?

MICHAEL: I did. In my early days on the ASM Education board, Stanley was president of our society at the time and he asked me to chair the search committee that was looking for a replacement of the education board, Fred Fender had timed out and Stanley was looking for someone as good as Fred or better, and we ended up getting a new head of the education board and that individual ultimately became one of the society’s presidents and that was Cliff and I’m blanking on Cliff’s last name.

VINCENT: I knew Stanley, I met him the first time back when I was looking for jobs back in 1981. I interviewed, he was chair of microbiology at Stanford and I interviewed and he offered me a position and I ended up coming here to Columbia.

ELIO: (laughs)

MICHAEL: As opposed to California?

VINCENT: Yeah. I really didn’t want to go—the reason I didn’t go was because there was really no virology at Stanford at the time, and here there was at Columbia and I made the right decision because I had a lot of good collaborations here. However, now I would like to be in California. At this point in my career it would be nice but of course it’s too late. And the funny thing is many years later, I think fifteen years later, I visited the same department at Stanford and there was someone there who was a faculty member. And he was a student when I visited and he remembered me saying “I don’t want to come here, I don’t like palm trees.”

ELIO: (laughs)

VINCENT: Anyway, so Stanley was a lot of fun. And after that I knew him, I saw him at meetings, and he was just a wonderful speaker.

ELIO: Really a major figure, no question.

VINCENT: And I want to refer to a blog post he wrote for Small Things Considered. We’ll put a link in the show notes. Everyone should read it, it’s called Fecal Transplants in the Good Old Days.

MICHAEL: And the ASM president and former chair of the education board was Cliff Houston. I don’t know how I could forget Houston, but I guess I’m blanking on cities today. But the other thing we should mention about Dr. Falkow is that before he became Dr. Falkow he was a medical technologist.

ELIO: That’s right.

MICHAEL: Of the ASCP. So he really did bench level microbiology for a long period of time and I got to know him pretty well at a Gordan Conference. It was the year that ASM had a Gordan conference in honor of education and I was one of the speakers at that meeting and I remember having breakfast with Stanley and we were talking about or lamenting about the cost of sequencing and finding virulence mutants and he shared with me his quick and dirty way of finding a strain of bacteria that would have a pathogenicity island. And this was at the time pathogenicity islands were emerging and people were beginning to understand the importance of them. And he said “I always knew it was about the IS elements! I always knew!” And he would just scan for these insertions.

ELIO: This guy’s been trained in clinical microbiology. He was a wonderful geneticist.

MICHAEL: Oh, absolutely.

ELIO: He really was responsible for us understanding plasmids the way we do in a major way.

MICHAEL: He and Allan Campbell, and if you have not yet seen Elio’s tribute to Allan Campbell I encourage you to go over to Elio’s blog and take a look at the fine piece that Elio wrote about Allan Campbell.

ELIO: Thank you.

MICHAEL: You get to learn of the wonder of the US Draft and all the wonderful things that it did. That was a great piece, Elio.

ELIO: Thank you very much, I appreciate that.

MICHAEL: I really enjoyed reading it and I learned things I had not known about either you or Dr. Campbell.

VINCENT: I heard a quote from Stan Falkow last week. He said, this is pretty funny and it’s also good: The goal of a bacterium is to become bacteria.

Michael and ELIO: (laughter)

ELIO: Lovely.

VINCENT: That is typical of Stanley, right?

ELIO: It sounds like him.

MICHAEL: I think it’s the goal of humans too.

VINCENT: To become humans, I don’t know. Not everyone, you know. Not everyone.


VINCENT: I want to tell you about the upcoming meeting called ASM Microbe, the annual meeting of the American Society for Microbiology. Anyway, this year it is in Atlanta, Georgia and ASM has a special opportunity for our podcast listeners. Get fifty dollars off registration for Microbe 2018 which is June 7-11 in Atlanta, using the promo code ASMPOD. ASM Microbe 2018. And next, scientists with their science and showcases the best microbial scientists in the world. Delve into your scientific niche in eight different tracks. Visit and use the promocode ASMPOD, all one word, for fifty dollars off registration. Alright, now for our science. We have a snippet from Elio.

ELIO: I got a snippet. Man, do I have a snippet. Listen to this title.  Converting Escherichia coli into an archaebacterium with a hybrid heterochiral membrane. And it’s by ten authors who I’ll mention the two top and the two bottom ones.  Antonella Caforio, Melvin F. Siliakus, and at the other end Arnold J. M. Driessen, and John van der Oost. All from Harlan, many from Groningen actually. Anyhow, get this title. Converting Escherichia coli into an archaebacterium. Right there, there’s a problem. Why archaebacterium and not archaea? Well that is for the authors to decide. They don’t go into that. But the idea is that if you were to look into the differences between archaea and bacteria, many stand out but high on the list is difference in the lipids.

So bacteria have regular phospholipids the way we know them. They have a phosphatidylglycerol to which the lipids are attached at the 3’ carbon just like it is sort of true for eukaryotes. Interesting. Whereas archaea have the lipids, the fatty acids or isoprenoids, first the 1’ carbon on the glycerol and it is by an ether link where in bacteria and eukarya is by an ester link. So these are very fundamental differences. In addition to which, and this is sort of an aside, there are some few archaea which have another puzzling thing. Instead of having a lipid bilayer they have a lipid monolayer. It is like as if the tails of the fatty acids were linked together. All of this put together is said to be because so many archaea are extremophiles. That is they live at very high pH or very low pH or very high temperature, high salinity, etc. They are not all extremophiles, some live in the rumen of a cow. But many are and so the idea is that the great distinction in lipids between bacteria and archaea has something to do with survival.

Now given then that you would never think that you could clone the genes for making this different fatty acid, different lipids, from the archaea into the bacterium, and therefore converting as the title says Escherichia coli into an archaebacterium with a hybrid hetero chiral membrane. So how do they do it? Well, they take a bunch of genes from both archaea and bacteria because the path overlaps some and put them into E. coli. They put it under a nice high-level expression system which consists of a lac promoter, which has IPDG or whatever, and you turn the thing on and you put it in an area of the chromosome of E. coli which is highly expressed, namely OriC, the origin of replication. It happens to be very convenient for cloning purposes. So now, first of all let me back off a second. Lipids always get, not always, often get a low exposure in the scheme of things. If you don’t need them you forget about them.

MICHAEL: That’s right.

ELIO: So I believe that they need the proper respect and they deserve a better place in the biological limelight, so I welcome the emphasis on this. But to believe that you can do this, that they converge in E. coli, in the host in archaeal regard to the lipids, is really a fantastic stretch. I mean it shakes your faith in something. Is nothing sacred?

MICHAEL: (laughter)

ELIO: So here we are. Anyhow, they do this and they figure out that if they do it the right way and play around with, and it is complicated and I won’t go into that, this being a snippet, but they get up to thirty percent of the lipids in the engineered strain to be archaeal lipids. That is significant. It throws out that the enzymes involved in making and putting fatty acids on the 3’ position and the 1’ position of phosphatidylglycerol are unrelated. So it is not a question of borrowing a little bit from a cognate enzyme. They are very different enzymes. They also tamper with the polar head group to make everything kosher and so they end up with this incredible result in the E. coli which has thirty percent lipids that it shouldn’t.

So what is it like to be an E. coli with this sort of lipid? Well, it depends how much you induce it because you can induce it to various levels by adding different concentrations of the inducer. And if you do it at moderate amounts which still have a lot of lipid, the thirty percent comes from that, the bacteria are said to grow at about the same rate as the parent strain. Let me take a break here. I have a real bone to pick here because they show growth on a linear plot. I don’t know why they do that because growth is exponential. So when you look at the plot you can’t tell, you can’t compare one with another. But that’s what they say, so let’s let it go.

MICHAEL: Yeah, I don’t know how they can get an OD of five and a half.

ELIO: Oh my god, that’s another thing. Everything is done at enormously high concentrations of bacteria where growth is not exponential. So I have no idea whether in fact this statement is correct or not, but let’s live with it and go with it. So what else do they know about it? They know that if they overexpress these genes things are not so nice. The cells become elongated, they become funny looking and they grow more slowly as well. So you can’t just keep pumping cells full of lipids that don’t belong to them. But you can do it reasonably and get a system which is amazing. It is nothing short of stunning. A bacterium which tends to be an archaea in part.

So what else do they know? They know that these cells are indeed more resistant to environmental challenges. For instance, they withstand exposure to a higher temperature, fifty-eight degrees whereas the control strains don’t survive fifty degrees. I’m talking about centigrade. They are also better able to survive freezing and thawing as well as exposure to butanal. I will say that this kind of work is going to be followed up. It needs more work but right now the indications are that these engineered organisms are in fact have greater resistance and therefore maybe higher fitness. And as they say, this has possible biotechnological applications because if you can make the cells where you have engineered something inside besides this—

MICHAEL: Well fifty degrees! Just look at the temperature profile. You can transform things at higher temperatures and make it just so much more efficient. And that swapping out the ether linked lipids for the ester linked lipids, if that gives you a delta of at least ten degrees C in temperature, it can make efficiencies of fermentations as you try to mass produce useful products and it is really fascinating. The other thing I found interesting is how they started it with introducing the audience to Luca. Luca is the last universal common ancestor and just thinking about Luca and the fact that the bacteria and the eukarya have these ester linked lipids whereas the archaea are using these ether linked lipids and they actually sort of tease you and tell you that in ancient times, when the common ancestor was around, there was some thought that the way cells may not even have had membranes, they may have been using such heretical things such as iron to contain cellular processes. So with these iron sulfate structures—

ELIO: They spend a fair amount of time introducing the whole paper by going through this and I mean that is perfectly legitimate and they’re entitled to do it in review of the amazing results, but I would say that all of this is still…

MICHAEL: Theoretical.

ELIO: Speculation.


ELIO: And speculation is fun but best done over a beer.

VINCENT: (laughs)

MICHAEL: Well, the Netherlands make fine fermented products so you can have many beers in Holland and think about these things.

ELIO: Maybe that was how this comes about. Anyhow, this is an amazing paper and it does talk if anything about the incredible plasticity of bugs like E. coli. We discussed, didn’t we, a paper where somebody cloned a gene for a single protein from a eukaryote and we convey them into an E. coli. Do you remember what this was?

MICHAEL: Yeah, we talked about it, yeah.

ELIO: So this was totally incredible because cloning a single gene for a protein that is essentially a membrane protein makes the E. coli replete with membrane vesicles. I mean it is nothing but wall to wall membrane vesicles. And this is a single protein, a single gene that needs to be cloned. So we are not done with amazing stories like this and I would say that tuning in on the microbial world is well worth doing.

VINCENT: Tune in.

MICHAEL: Tune in!

VINCENT: So Elio, getting back to the title, I think they call it an archaebacterium because it is a hybrid, right?

ELIO: Well yes, but when you do that you should explain it. I think they could have done well, I don’t think it appears as archaebacterium, I am not so sure it appears again in the paper.

MICHAEL: Anywhere else in the text.

VINCENT: That’s true.

ELIO: I think it would be good if they, yeah, it’s…(laughs)

VINCENT: But that’s the old name for archaea, they used to call them archaebacteria.

ELIO: Yes, it is, but archaea, I mean, the people who are such a champion for the concept of the three arms of life, domains of life, would shudder at the term because to them it means there is something in between. Well, obviously this paper says you can make something in between, but I think I would be careful with the term.

VINCENT: I think the idea of converting is a little bit of a stretch, right, because they provided it with a very different membrane and that’s about it.

MICHAEL: But the ribosome is still a bacterial ribosome, it’s not a eukaryote.

ELIO: Absolutely.

MICHAEL: All the rest is E. coli and they didn’t do the archaeon ribosome or any of those other things, but that may be their ultimate goal to see if they can really goose the system to get it to go like an archaeon. But again, it gives the initial reader of microbiology some insight as to why methanogens would benefit from having these ester linked lipids or, excuse me, ether linked lipids because they make them more resistant to solvents.

ELIO: But they do, methanogens are archaea.

MICHAEL: Yeah, that’s what I meant, that’s why they’re in the cow’s rumen is because of the solvents that are being produced from the fermentation products that are coming out.

ELIO: That is true also for high temperature. Many archaea are hyperthermophiles, it goes for all the extremophiles of archaea, they all may benefit from having their own kind of lipids. It just makes sense.

VINCENT: Alright, thank you Elio.

ELIO: My pleasure, this was fun.

VINCENT: I have a paper for you from Cell, it is called Microbial Genetic Composition Tunes Host Longevity. And this is all about trying to live longer, at least for worms.

ELIO: If you’re a worm.

VINCENT: If you’re a worm.

MICHAEL: If you’re a worm!

VINCENT: I think humans do pretty well already, right?

MICHAEL: Yeah, we make it to ninety! We make it to at least ninety. Our goal is to follow Elio.

VINCENT: The first author here is Bing Han, and the last author is Meng Wang. And this is from Baylor College of Medicine and the University of Texas, both in Houston. And the idea here is that there is some evidence that our gut microorganisms are linked to the aging process in some way and the idea is that the microbiome makes metabolites that are important but also can deal with exogenous chemicals that may be harmful and we know for example that there are changes in the microbiome as you age and there are diet driven changes in the microbiome that help your health as you get over. But this is all mostly observational and correlative and they wanted in this paper to try and get some direct evidence for the role of the microbiome in longevity.

MICHAEL: And these experiments are hard to do. And as they introduce us to this concept there is one line that you gotta keep in the back of your head as Vincent begins to reveal their data, and you have to keep in mind or bear in mind that the mammalian gut microbiota is of high complexity and there are profound technical challenges in isolating specific prolongevity microbial variations just by getting the sample out of a mammal in the nick of time.

ELIO: Aint that the truth. I totally agree with you and it has to be said over and over and over again because the microbiome is part of the headline of the newspaper, and the claims that are made are even if they are couched in tentative terms, to me they sound like hype.


VINCENT: Yeah, true.

MICHAEL: And we have to be very careful, but this is a very careful and well-conceived, laid out study.

VINCENT: So in part it is because they start with a very simple model organism, C. elegans, the wonderful soil nematode that has been a mainstay in many labs because it has a defined number of cells. We know where each cell comes from, and for this paper it is genetically manipulable, as you will see there are tons of mutants available with all sorts of phenotypes. And it is easy to grow in the lab, and it has one microbe in its gut microbiome. E. coli. And you feed C. elegans E. coli and that is what ends up in the intestinal lumen. A gut microbiome of n=1.

MICHAEL: It’s the ideal model system.

VINCENT: Right. And what they do here is they say we have an E. coli, a K-12 strain. We have a library where each isolate has a single gene knockout, so these are genes that you can knock out and the E. coli will still grow. And there are 3983 such E. coli mutants. And they simply ask if we feed each of these to C. elegans from when it is born to when it becomes an adult, what happens? So they go through 3983 E. coli mutants and they grow C. elegans on each one of these and they ask if there are any that prolong the life of C. elegans. And if you are wondering how long C. elegans lives, it’s about 25 to 28 days or so, looks like from these graphs. And then you can look at a few days, 5-6 days increase, and that’s what they do. So they go through this whole library and identify 68 mutants which, again, when fed to C. elegans they prolong the lifespan. So they validate these, they get it down to 35 mutants, they reintroduce those to make sure that they still work, and in the end they have 21 mutants that make C. elegans live longer.

MICHAEL: And you should point out that these are deletion mutants, so they are taking something away from the bacterium that then allows the host to live longer.

VINCENT: Correct. That’s right. Alright, so you can provide these bacteria to C. elegans when they are already adults—

MICHAEL: Because they’re eating them.

VINCENT: So in other words if someday this works on people, you and I, Michael, could take whatever it is they’re going to develop and it might help us in our old age. But I’m much older than you, you’re a young guy.

ELIO: (laughs)


VINCENT: So 21 mutants, and they prolong the life, the bacteria, and these genes that are deleted are in all kinds of classes. They have a table here. They’re transcription, translation, metabolism, respiration, membrane transport, proteases, chaperones, all sorts of things. So they’re all over the place, not just one thing.

MICHAEL: And then the famous unknown genes, or the “other”.

VINCENT: So now they do a series of experiments that leverage these twenty some E. coli mutants and also C. elegans mutants because there are lots of those as well.

ELIO: The numbers are pretty impressive because some of those mutants extend the lifespan by a factor of forty percent.

VINCENT: Yeah, that’s good. If you’re a worm you could be happy about that right?

MICHAEL: Yeah. (laughs)

VINCENT: So first of all they ask, would these work in a sick worm? Would these help sick worms not be sick? And they have two models where one mutant of C. elegans, you get germ line tumors and death, and in fact if you introduce 16 of these bacterial mutants into that mutant C. elegans it increases their survival. So if the worm is going to develop a tumor, these E. coli will help it live longer. And the other model which is interesting, they have a model for Alzheimer’s disease in C. elegans. They put in an altered beta amyloid protein coding gene, and these C. elegans die early, they have trouble moving around, and if they put the bacterial mutants into them, 14 of the 29 prolong the lifespan of these transgenic C. elegans strains. So, in other words, not only do removing these genes from E. coli make the worms live longer but they can also make them live longer in the background of specific pathologies like tumors and amyloid beta accumulation.

MICHAEL: And that’s at the germ level of the animal, if you will.

VINCENT: Yeah, it is. Now next, what’s going on here? It’s already been studied in many labs, what makes worms live longer, and there are a number of mechanisms. Two of them are the insulin like growth factor pathway and the target of rapamycin signaling pathway, and caloric restriction. I don’t know if everyone knows this, but did you know caloric restriction can prolong lifespan?

MICHAEL: It’s certainly been demonstrated in mice.

VINCENT: Yeah, it’s amazing, you eat less. Caloric restriction in laboratory animals prolongs life. It’s quite clear. In our American culture we tend to eat a lot, so it might not be a bad idea to cut back what we eat.

ELIO: It’s a widely held view.

VINCENT: I just love food, you know. It’s hard. Okay, so then they look at some of these pathways. They have mutants which disrupt this insulin like growth factor pathway, the mTOR, and the caloric restriction, and in fact they find that some of these bacterial mutants cannot prolong the lifespan of C. elegans on the background of these mutations in the other pathways. In other words, suggesting that they are working through the same pathways. So that is a very nice genetic approach, right? You take out the bacterial gene, the C. elegans gene, if you don’t get longevity any more, extension any more, they must be in the same pathway. Pretty cool.

Then they look at caloric restriction and say, do these bacterial mutants have any effect on eating or defecating? Which are two things that are known to regulate to effect longevity in the worm. And they decide that these bacterial mutants do not affect pharyngeal contraction or defecation. So they don’t think that these are contributed, that these bacterial genes are contributing to those activities. In the course of this study they find that there are two bacterial mutants in two separate genes which regulate the biosynthesis of colanic acid, or CA, and this is a polysaccharide secreted by many enterobacterial species including E. coli K12 that we have here. And there is a biosynthesis gene cluster that regulates the production of colanic acid. There is a central transcriptional activator called RCSA, and there is a protease called LON. I’m sure that Michael and Elio remember LON for other reasons.

MICHAEL: Oh, that’s Matt Gottesman’s work, isn’t it?

ELIO: Oh way before that, way before that. It goes back to the people in the PAR institute.

VINCENT: So, LON is a protease that can repress the biosynthesis of colanic acid. So the idea is that overproduction of colanic acid is what is happening in these bacterial mutants. So they first look at colanic acid levels and they find that bacterial mutants lacking the LON protease and another gene that is a positive regulator of that, they have higher colanic acid secretion. So you take out the RCSA gene which is the master regulator of colanic acid biosynthesis. You suppress the production of colanic acid. And if you put all these mutants together they complement each other. So if you take away the protease it will suppress the problem caused by the removal of the transcriptional regulator. So in other words there is a cluster of genes involved in the synthesis of colanic acid and they think that this is involved in prolonging life.

MICHAEL: So Vincent, let me ask you, so Roy Curtis if my memory is serving me right, published a paper maybe 5-6 years ago on colanic acid in which he was showing that it was needed to promote biofilm formation and one of the things I always associated with biofilm formation is that the microbes are essentially quiescent. They are not metabolizing or doing anything. So do you think that could be impacting longevity as if it is going to promote E. coli to form a biofilm in the gut of the C. elegans or? So I was spinning thinking about this and I am trying to make the connection of why colanic acid? Are we going to run out and all get colanic acid tablets and begin to take them?

VINCENT: Well, I think at the end of this paper that’s what (laughs) that’s what they’re saying, maybe we should take colanic acid. I think it’s not a biofilm because they show it in the next set of experiments. You can feed the C. elegans colanic acid and it prolongs their life. You don’t need a biofilm. So the bottom line here so far, we have a number of bacterial mutants that give C. elegans a longer life and some of those genes that are deleted are involved in the synthesis of colanic acid. So there is a link here between colanic acid production and living longer in C. elegans. And they also think that there is a link with mitochondria in these mice—mice (laughs)

MICHAEL: Worms! These are worms!

VINCENT: I know, I’m used to saying mice.

MICHAEL: No legs! No legs!

VINCENT: So one of the hallmarks of aging is mitochondrial dysfunction in the body wall muscles of C. elegans. And this happens when the mitochondria fragment. And they can take pictures of the muscles of these C. elegans and you can see the mitochondria fragmenting as they age. And in fact if you give the C. elegans these colanic acid overproducing bacterial mutants, it attenuates the mitochondrial fragmentation. So that’s somehow another link to making the worms live longer. They also show that this works in other nematode species that are a hundred million years diverged from C. elegans, so it is not just a C. elegans thing. So that is pretty neat.

So the next series of experiments they get purified colanic acid and they give it into E. coli and it prolongs their life. It prolongs the life of E. coli, works with a number of bacteria that you feed to C. elegans. So in giving worms colanic acid also delays the mitochondrial fragmentation. It helps the worms to move better. It helps get rid of tumors. It decreases the beta amyloid problem. And guess what? It even increases the life of fruit flies!

MICHAEL: Yeah! That was what was remarkable and we’re talking about wild type Drosophila living as long as 90 days for a small fraction of the population.

VINCENT: So I have to know, what’s with mice? Let’s feed mice colanic acid, right? Let’s find out what’s nice. So colanic acid, if you’d like to know what it is, it is a repeating unit of glucose, galactose, fucose, and glucuronic acid decorated by pyruvate and acetate. What an interesting molecule.

ELIO: Go out and buy stocks and people will make colanic acid.

VINCENT: That’s right.

MICHAEL: It almost could be peptidoglycan, it’s repeating subunits of simple carbon.

ELIO: It’s not the correct length though, is it?


VINCENT: No, it’s not.

MICHAEL: It’s not crosslinked.

VINCENT: But they made monomers of colanic acid and the monomers don’t work to extend lifespan. They have to be multimers. So you can, the colanic acid doesn’t affect the bacteria. They did a number of experiments to look at that, and in fact you can inactivate the bacteria and feed it to C. elegans along with colanic acid and the colanic acid still works. Now here is a very interesting experiment. They have mutants of C. elegans that are defective in endocytosis, which is a way of taking up material from the cell exterior and these mutants cannot have their lives prolonged by giving them colanic acid. Apparently, you need to, the worm needs to endocytose colanic acid to have this prolonging of its life. Really interesting.

The next series of experiments they find a connection between colanic acid and mitochondrial fragmentation. In fact, they have a couple of worm mitochondrial mutants. They have a mutant which is defective in mitochondrial fission, which is the breaking up of mitochondria, the dividing. And then they have a mutant defective in mitochondrial fusion. And they want to know does the colanic acid work in each of these? And what they find is that it does not work in the fission mutant. The mitochondrial fission mutant. Somehow mitochondrial fission is important in this prolongation of life in worms.

ELIO: Do they have a clue as to why?

VINCENT: Yeah. In the next series of experiments they think that there is an unfolded protein response in the mitochondria. So to tell you a little about that, unfolded protein response, I am familiar with in in the endoplasmic reticulum of eukaryotic cells where, if there is some kind of stress on the organism by making different viral proteins in the ER, you will have a response to shut down translation because the cell does not want to make misfolded proteins.

So apparently there is one in the mitochondria and they think that the colanic acid is inducing this unfolded protein response and then the effectors that come in to try and fix that are the ones that prolong the life. They don’t really know what they are, but they think that is the mechanism of prolongation of life. So in other words they address this by looking at some very interesting C. elegans mutants that are defective in these unfolded protein responses and the effect of bacterial colanic acid on extending the life of the C. elegans requires the mitochondrial unfolded protein signaling pathway.

So the idea, Elio, is that the unfolded protein response, the effectors of that response must be somehow involved in prolonging the life. It’s kind of counterintuitive that you would need mitochondrial fission to do this, but I think it is because it stimulates this unfolded protein response.

MICHAEL: Where you effectively get a new mitochondrion. Because when you fis– you’re effectively making a new one and so you effectively are starting over and your mitochondria is not effectively senescing or having mistakes or not doing what it’s supposed to do.

VINCENT: That could be part of it as well.

MICHAEL: So the colanic acid is effectively telling the cell hey, you better divide because things are bad, and it may be something simple like that, and it also makes sense why the endocytosis mutant does not work, because the colanic acid is not getting in to effectively stimulate the mitochondria.

VINCENT: Well that could be, or if you don’t have the right bacteria that are producing it, right? Or if the microbiome is changing as you age, maybe you lose the colanic acid producers. I’m sure it’s more complicated than that, right? This is one, these were a handful of bacteria that they focused on.

MICHAEL: And it is a very, very simple microbiome because it’s just E. coli.

VINCENT: Yes, yes. In fact they point out that when they look at the genes involved in producing colanic acid they also see genes involved in chorismate metabolism which is a precursor for aromatic metabolites and it is known that deficiencies in two chorismite derivatives, ubiquinone and folate, are why E. coli mutants that have been previously studied are able to prolong the host lifespan of C. elegans. Now there is a drug called metformin which interferes with bacterial methionine biosynthesis is also coupled with chorismite metabolism and that extends life of C. elegans. So they say that chorismate biosynthesis in your microbiome may be another way to promote host longevity in a broader sense because it wouldn’t involve just colanic acid.

MICHAEL: And metformin is one of the most prescribed drugs on planet Earth for types with Type II Diabetes.

VINCENT: Is that right?


VINCENT: So they say in the discussion, colanic acid may provide an exciting approach for improving human health and longevity. Now, I don’t know. I think, as we said earlier, humans can live long. The question is how healthy you are as you age, so maybe you could address some of those issues with something like colanic acid or something more.

MICHAEL: Well, we have a large cohort of folks over a hundred, we have a large cohort of folks over ninety, eighty, etc. We could effectively measure the colanic acid in those individuals and just ask the simple question, what does the population look like? If it varies all over the place, a simple correlation experiment may be the first step.

ELIO: I think I could donate.

MICHAEL: You’ll donate?

VINCENT: (laughs) Now they end up with a very interesting point here and that is of course mitochondria came from bacteria and they share metabolic pathways with bacteria. So it is interesting that the bacterial colanic acid that they study here that one of the targets at least appears to be mitochondria. So, you know, is that a remnant of a previous property? Who knows. It is very interesting.

ELIO: Are we witnessing a family reunion?

VINCENT: (laughs) Gut bacteria of C. elegans make colanic acid, it induces mitochondrial fragmentation, and it turns on this unfolded protein response, and then that makes some signals that improve host fitness. And that is the big question, what are those signals? Let’s find out what they are and maybe we can move up the evolutionary ladder here. Look at mice, and rabbits, and then humans, I guess. Anyway I thought this was interesting because you have the genetics of E. coli and C. elegans combined here to solve this problem. Really neat.

MICHAEL: And it’s a whole new world of crosstalk. I mean, the microbe, the bacterium, in this case E. coli is talking to an eukaryotic symbiote, the mitochondrion which once upon a time was a bacterium.

VINCENT: That’s right. Now Elio, you must have lots of colanic acid.

ELIO: I’m loaded with it.


ELIO: You want more of colanic acid.

VINCENT: Alright. Before we wrap it up, just a couple of emails here. The first one comes from Amir.

Hey guys, hello from sunny Israel. 83 F, perfect beach weather. Thanks a lot for the podcasts, I am really enjoying them. I am hearing a lot recently about the E. coli outbreak in romaine lettuce and was wondering, do you know how they trace the source and the specific bacteria? I mean a person who gets sick suffers from diarrhea, vomiting, and severe stomach cramps and can lead kidney failure. This is a very general symptom of enteric disease from what I know and if you take a look at the gut microbiome there is a good chance of finding very similar strains of E. coli in there. So how do they clinically differentiate the strain? How do they trace it back to the specific lettuce growing area? Thanks again for the great work both on TWIM and on Small Things Considered.

ELIO: Thank you.

MICHAEL: Well, that’s good old-fashioned shoe leather epidemiology. They actually go out and they interview folks who have gotten sick and this is the CDC and the local public health departments associated with states where individuals have been reported ill and the CDC will actually call you. My brother got sick once at a wedding and he and his wife got called by CDC epidemiologists inquiring what they ate, when they ate it, when they got sick. And it’s good old-fashioned shoe leather epidemiology. And then, based on what you report to the CDC, they may elect to ask for stool samples depending on whether or not you have had antibiotics, and in this particular case with E. coli OH157H7, the O stands for the O antigen which is in the outer membrane of the E. coli. And the H is actually the type of flagella protein that this particular E. coli is having. So, that license plate is actually a description of the car that hit you, it is responsible for the diarrhea that you are getting.

And the way that they trace it back to the particular farm, and in this case it is in Yuma, Arizona. And this must be one of those mega factory farms because it seems to have supplied twelve states and a large number of restaurants and stores and it’s really caused a great deal of concern. I saw a report of it on our local news last night and they had folks who are still worrying about it happening here in South Carolina where this is the height of tourist season. And again, the CDC and our local public health department is very much concerned, but the general guidelines out there on how to protect yourself is simple hand hygiene, wash your hands, don’t prepare food or drink for others when you are sick, keep hot food hot, cold food cold, cook your meats thoroughly to kill off this nasty variant of E. coli, and avoid raw milk and other unpasteurized dairy products and unpasteurized juices.

Fortunately, for most of us in the US we only consume pasteurized milk and pasteurized juices because we have learned our lesson with unpasteurized products and again, this is one of those types of food poisoning for which you do not need an antimicrobial because if you do, it can often result in you developing hemolytic uremic syndrome, where the microbe actually dumps more toxin based on your exposure to the antibiotic. So you don’t necessarily want, if you have got old antibiotics in your medicine cabinet you don’t want to take them because they may not do the trick.

VINCENT: So Michael, the difference between O157H7 and E. coli in your gut is also a lot of other DNA, right?

MICHAEL: Oh yeah, so it’s forty percent different in DNA sequence and garden variety E. coli K12. Forty percent different in its DNA, yet it is still E. coli.

VINCENT: Do they use that to diagnose at all?

MICHAEL: Yeah, what the CDC is ultimately doing today, years past they would use pulse field gel electrophoresis which is effectively that molecular fingerprint that you see on many of the crime TV shows. But today what they are resorting to is DNA sequencing to identify the culprit. And they are looking for the particular toxin gene for this hemorrhagic toxin that actually came from Shigella on a pathogenicity island.

VINCENT: So Michael, what is the source of the E. coli in the lettuce? Is it contamination?

MICHAEL: It’s water. It’s either water contamination because it’s not potable water that they use to irrigate the fields. As you can well imagine, lettuce is a vegetable that has a very, very high water content. It gives it its crispness, and if you are buying the prepared lettuces it can also be a function of the wash water. If the product has been contaminated and the fecal material spreads in the wash tank the E. coli can effectively multiply, and when the temperatures are right as you are transporting it home or if it doesn’t stay cold in the cooler at the store, and all of these other things can come in to mix it up. And the other thing about E. coli 15787 is for the garden variety E. coli that typically give us traveler’s diarrhea, you need to consume about a hundred thousand of them in order to become ill. With this variant of E. coli, you need many, many fewer, typically between a thousand to ten thousand. So you need far fewer.

ELIO: Are they more acid resistant?

MICHAEL: Not necessarily. The virulence factors are just so much better at invading your gut and infecting microvilli because the pathogenicity island it has.

VINCENT: So what is the ultimate source of this E. coli? Cows?

MICHAEL: Probably. Fertilizer, manure, whatever—

VINCENT: You could also get it from hamburger, right?

MICHAEL: You can get it from hamburger but there it is a direct result of inefficiencies and slaughtering and how many cows went into making that hamburger. If you go out to a fancy restaurant, how many cows were involved in the production of that hamburger? The rule of thumb is you want one, but typically you sometimes can have between ten and a hundred different animals in the ground beef that is supplied to commercial restaurants.

VINCENT: So what you should take home from this TWIM is that you should eat a lot less so you can live longer and eat a lot less of these things that we’ve talked about.

MICHAEL and ELIO: (laughter)

MICHAEL: That can make you sick.

VINCENT: Yes. Eating is a risk factor. (laughs)

MICHAEL: It’s one of the hallmarks of the twentieth century. We’ve really cleaned up our food supply and while diarrheal diseases are still the number one killer on planet Earth, we’ve actually improved a lot in the 20thand 21stcentury.

VINCENT: Yeah. Alright, Cliff writes:

Dear all, I am a neuroscientist with an inventor’s interest in both biology and technology, so I listen with delight to both your podcasts TWIV and TWIM and to your predecessor’s podcasts TWIT and TWIG.

TWIT is This Week in Tech and TWIG is This Week in Google. And of course, they are both produced by Leo Laporte, who was the inspiration for me to start doing This Week In series. So thank you for that. And finally, Justin sends us an article published in Science.

By wrapping itself in antibodies, this bacterium may become a stable beneficial part of the gut.

ELIO: Yeah.

VINCENT: This is a cool summary of a story where they find that a gut bacteria, I’m looking for the—what’s the bacteria? Bacteroides fragilis. Its ability to stay in your intestine requires IGA which coats the bacterium.

MICHAEL: And IGA is our most produced immunoglobin, its like 40% of our immunoglobulins produced on a daily basis.

VINCENT: So the IGA coats the microbes and allows them to clump together along the gut lining and penetrate the mucous layer. It allows them to stay right next to cells, and without IGA the microbes fail to colonize the gut. Very interesting. That is microbiology, it’s an amazing field. Thank you, Justin. Alright, that is TWIM 176. You can find it at any good podcast app on your phone or tablet. Just search for TWIM and subscribe so you get it every week. If you like what we do think about contributing, just a dollar a month will really help with our expenses. You can find out more at And we love to get your questions and comments, send them to Elio Schaechter can be found at Small Things Considered. Thanks, Elio.

ELIO: My pleasure, thank you.

VINCENT: Michael Schmidt is at the medical university of South Carolina, thank you Michael.

MICHAEL: Thanks, everyone!

VINCENT: I’m Vincent Racaniello, you can find me at I want to thank ASM for their support of TWIM. Ray Ortega for his technical help, and Ronald Jenkees for the music you hear on TWIM. Thanks for listening everyone, see you next time on This Week in Microbiology.


Content on This Week in Microbiology ( is licensed under a Creative Commons Attribution 3.0 License.

Transcribed by Sarah Morgan.