This Week in Microbiology

With Vincent Racaniello, Elio Schaecter, Michael Schmidt, Michele Swanson

Episode 173: Gee whiz with style

Aired March 30, 2018

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 173, recorded on March 28th2018. I’m Vincent Racaniello and you are listening to the podcast that explores unseen life on Earth. Joining me today from Small Things Considered, Elio Schaecter.

Elio: Well hello there!

Vincent: Good to hear you again.

Elio: Nice to hear you.

Vincent: Also joining us from Ann Arbor, Michigan, Michele Swanson.

Michele: Hello!

Vincent: How are you, Michele, everything well?

Michele: Everything is great, my team has gone to the final four.

Michael: We were waiting for that.

Michele: (laughs)

Vincent: You know, Michele, I saw your president at a meeting last week and he said, I’ll take credit for the victories so far but if they lose in the future it’s the coach’s fault.

Michele: (laughs)

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

Michael: Hello, everyone!

Vincent: How are you?

Michael: I’m well.

Vincent: Very good. Today we have a snippet and paper. And first, I have a followup email from Bill who writes:

In your excellent recent podcast about finding new calcium dependent natural antibiotics in soil samples, Vincent mentioned that your wife used to collect samples while you were traveling. It struck me that this is an excellent citizen science activity, travelers would use an app to ask if they were in an interesting location and could photograph and collect the sample in something like a sandwich bag and label it with an app supplied identifier. I would certainly do this in my travels and I am sure many others would as well. A quick web search for citizen science soil collection antibiotics shows that this is already been thought of, and I think your listeners might be more interested than most in participating. An in depth examination of the text of the first page of Google results that this may have started only last fall. And this is from Bill, a science guy on a farm in Flemington, New Jersey.

Michele: Cool.

Elio: Nice.

Michael: Just outside of Princeton, isn’t it?

Michele: Yep.

Vincent: It’s not too far from me.

Michael: Yeah.

Michele: So who is collecting the samples and doing the analysis, does it say?

Elio: No.

Vincent: He didn’t provide a link.

Elio: I hate to throw some cold water on this but collecting samples for the sake of looking for soil samples, looking for antibiotics, has probably been saturated. There is of course endless numbers of soils, but the number of soils that have been investigated has been huge. So I don’t know that this is going to be the fertile ground for finding new antibiotics.

Vincent: In Michael’s story last time it was, right Michael?

Michael: It was indeed.

Elio: They found something, yeah, that is true.

Michael: But it was a screen as well.

Elio: Finding new samples of soil, dependent at looking at what you have in a different way.

Vincent: So you would argue that what we have is enough?

Elio: Yeah, enough, you never know, but look there is a whole five story building in Tokyo, Japan in order to do that. That’s all they did, they look for samples everywhere, and you know, that approach, if you don’t know how to look better, getting more samples isn’t going to do much.

Michele: But the better–

Elio: Citizen science activities are wonderful and they should be encouraged, so I hate to do this, I hate to say this. But I’m not sure that this is very…

Michele: I’m thinking that the fact that we can now do it with this non culturable strategy might be motivation to go back and look at those samples.

Michael: Certainly to dig them out again.

Elio: That is the question, looking at the samples differently, not getting more samples.

Michele: Right. I see. Right, right. Got it.

Vincent: Okay. Well there you go. Thank you, Bill. And if anyone is interested, search google for, yeah if you do a google search citizen science soil collection you find dirt sample, the University of Oklahoma Citizen Science Soil Collection Program, bunch of different programs here. And so check that out. Thank you, Bill. Alright. It is snippet time here on TWIM and for that, I am going to hand it over to Elio and he will give you a title and I guarantee you don’t know at least one word in this title.

Michele and Michael: (laughs)

Elio: The title is: “Fertile Prototaxites taiti: a basal ascomycete with inoperculate, polysporous asci lacking croziers.” The authors are get authors Honneger R, Edwards D, Axe L, and Strullu-Derrien C, and it was published in the Philosophical Transactions of the Royal Society Series B. This is gee whiz in style.

Vincent: (laughs) Gee whiz in style.

Elio: There are on, in the world, fossils, which look like a big cylinder, huge cylinder, but ten meters long and one meter across. And they come from about four hundred thousand years ago, four hundred oops million years ago, in a time when the rest of plants were about ten centimeters high. Okay. So this is written up in our blog, Small Things Considered, under the title Humongousest Fungus, this is not a humongous fungus this is the Humongousest Fungus.

Michele: (laughs)

Elio: So why do I say that it is because the best guess is about the origin of what this fossils are, that they were fungi. People have argued all over, I mean they look like they could be tree trunks for a very large tree, but there were no trees at the time. So, I mean, the biggest thing there was was shrubs about ten inches high. So people have come up with all kinds of thoughts, but the prevalent thought and the one that I think is now accepted is they were fungi. Fungi ten meters tall.

Michele: Wow.

Elio: The landscape, they would look like sort of rockets poised for departure. So the landscape you would see then would be of this giant cylindrical structures standing upright and dominating the landscape like nothing ever has. So if you are into mushrooms and fungi like I am you have bragging rights about the fact that it was a time when nothing came close in size and majesty as these guys.

Michael: They were the redwoods of the microbial world. They still probably are the redwoods of the microbial world.

Elio: The redwoods of the world!

Michael: Redwoods of the world, that’s right!

Elio: So anything, there was nothing else like it. So what’s the story? So first of all, let me dispose of one big question, what did they eat? Fungi is saprophytic, they don’t have photosynthesis, they don’t make their own food. So the source of food could have been the brush underneath, but it is difficult to imagine enough brushes, enough shrubs, to be able to feed into this. So the idea which is appealing but has zero evidence is that this was actually more like a lichen in that it was a symbiote between fungi and some form of photosynthetic organism. Do you like the idea?

Michele: Yeah.

Michael: Yeah.

Vincent: Mhm.

Elio: That’s a good thing, but there’s no evidence for that. But nothing else would work unless you invent a new biology for fungi. Anyhow, so the discussion has been let’s agree they are fungi, maybe fungi plus, but right now just stick with the fungi part. And what are they made of, what are these? So there is a paper, the paper that I am discussing, talks about that these were ascomycetes. A previous paper which just appeared not long ago suggested they were Basidiomycetes. I imagine that most mushrooms are Basidiomycetes but at most, actually more fungi in nature like molds and yeasts which are ascomycetes. And the distinction is in the basidiomycetes and ascomycetes make different kinds of spores sexually. Basidiomycetes make them generally on the gills of mushrooms by cells called basidia which sort of butt out, basidia spores. Ascomycetes are made in asci, which are sacs, an ascos is a sack, and contains usually eight spores.

The evidence is basically that when you look and cut through this fossil, you find things that look like essentially that look like asci. However, the asci don’t contain eight ascos spores here, but they contain a huge number. And so about a hundred or so, and this is a problem of, it tells you it is not a regular ascospores or asci. But there are ascospores or asci known in extant fungi which have a lot of spores. So it is not an argument against it, just that it is different than what you look at today which is not surprising.

So this is quite the story, and I don’t know what else to tell you about it except that you should look at it, I think viewers or listeners should have a look at the paper and also go to the blog site because it shows the picture of, well actually, it doesn’t show a picture of, it’s an imaginary drawing, but it is a previous, we once published something, When Fungi Ruled the Earth, and that has a rendering of prototaxites, it is from 2007. But the rendering is still the same. So anyhow. There are no fungi like it today and here you have it.

Michael: Why do you think they died off?

Elio: Huh.

Michael: The why questions I know we can’t answer, but…

Vincent: Meteor hit the Earth.

Elio: It’s possible.

Michael: “Meteor hit the Earth” is the best example.

Elio: Well, it’s possible that when plants got to be serious about making big shrubs and trees that they out-competed them. But, you know, it happened afterwards, but it is a very good question. I have no idea. The story is so unlikely, I can’t go much beyond it in terms of my imagination figuring out what could have happened.

Vincent: Elio, what is a crozier?

Elio: A crozier is a structure in a, let me think…

Michael: It’s what the bishop carries as he walks down the aisle at church.

Vincent: The staff?

Michele: Structural.

Michael: It’s got a crook on the end so you could grab the lamb to bring it back into the herd. It looks most similar, to help you, Vincent, like Ebola. It looks like the Ebola virus.

Vincent: The curled top of a young fern.

Elio: Let’s stick with mushrooms, let’s stick with fungi. It is a structure that is found in the ascomycetes but not all. So not having croziers in this thing does not mean it is not an ascomycetes. I mean the title tells you that it lacks croziers. But croziers are structures at the base of asci. They look like the hook atop a shepherd’s staff.

Michael: Got it.

Elio: It’s worth noticing in the title, all it says that not all have them but many have.

Vincent: There’s not likely to be any DNA in these fossils, right?

Elio: Ah. Ah ha. This is really an interesting thing. The whole argument could be solved by one little tiny bit of DNA. And I don’t think anything that old has been found. But you know, it struck me that in a trunk, in something like a tree trunk that is one meter wide in the middle, who knows.

Vincent: Yeah.

Elio: I really think that it’s worth looking and I hope people do because one microgram of DNA or even less than that can solve all kinds of arguments. It could tell, for instance, is it one genome or several genomes? Is it a symbiont?

Vincent: I heard recently, someone told me there is a new technique where you can laser ablate single cell layers from specimens and immediately put them into mass spec and they have been doing this apparently with dinosaur fossils and they can find collagen traces in them.

Elio: That’s right, yeah.

Michael: You can also find out what color their feathers were.

Vincent: (laughs)

Michael: No, I mean I heard a talk from a paleontologist last year and he is taking his fossils out to the advanced light stores at Stanford and they’re doing exactly what you’re saying. They’re ablating and it goes through the cyclotron and it gets accelerated and they can figure out the elemental balance that was associated with the fossil and the metals that are associated with pigment remain and you can infer from the metals that they are able to detect from the X-ray spectroscopy what metal was there and hence the color of the feather.

Vincent: Neat.

Michael: Yeah.

Michele: Wow. I was impressed that these massive fungi have been found all over the world. North America, Northern Europe, North Africa, Western Asia, Australia.

Elio: They talk about there being 14 species. My god.

Michele: So they clearly were the dominant, or a dominant life form at that point.

Vincent: Yeah. They did well, they were the bullies, right?

Elio: Right. (laughs)

Vincent: Thank you, Elio.

Elio: This is good fun.

Vincent: Yeah, it is.

Michael: The oldest DNA that has ever been recovered as you probably recall was the 250 million year old halobacterial sequences from halite. So we have 250 million. We only need 150 million more years to get back to the fossils that–

Elio: I’m counting on all this massive structure.

Michael: Yes.

Elio: So when this got fossilized, maybe there was a way that you can argue that the DNA got spared somewhere in the middle of the trunk or something.

Michele: Deep inside, yeah. Stay tuned.Vincent: Stay tuned, exactly.

Michael: Stay tuned!

Vincent: I want to tell you about the upcoming meeting called ASM Microbe, the annual meeting of the American Society for Microbiology. This year it is in Atlanta, Georgia, and ASM has a special opportunity for our podcast listeners. This is not food, this is not hard drives, it is not videos. Get $50 off registration for Microbe 2018 which is June 7-11 in Atlanta using the promo code ASMPOD. ASM Microbe 2018 connects scientists with their science and showcases the best microbial scientists in the world. Delve into your scientific niche in eight different tracks. Don’t miss this opportunity. Visit, that is and use the promo code ASMPOD, all one word, for 50$ off registration. When you go to register you will see “do you have a promo code?” You type in ASMPOD. Now for something completely different.

Michael: Completely different!

Elio: Couldn’t be more different.

Michael: This is a fascinating paper that was published in Science Advances which is an open source document from the AAAS. And it is entitled “A commensal strain of Staphylococcus epidermidis protects against skin neoplasia.” And it is from the department of dermatology at the University of California San Diego, the Scripps Institute of Oceanography, also at the University of California at San Diego and La Jolla, the Jackson Laboratory for Genomic Medicine, and NIAID of our National Institutes of Health, and the authors were Nakatsuji, Chen, Butheer, Trozoss, Nam, Shirakawa, Zhou, Oh, Otto, Fenical, and Gallo.

Elio: Richard Gallo.

Michael: Richard Gallo, not Robert, the more famous of the Gallos.

Vincent: I would say the most famous is the vinyard, right?

Michael: Yes, yes, Ernest and Julio.

Vincent: Ernest and Julio, very good.

Michele: But with this line of research, don’t count Richard Gallo out. He’s making a run.

Michael: Oh, no, this is a fascinating paper. So here is the bullet. This reports the discovery that strains of coagulase negative Staph epidermidis which is a normal inhabitant of our human skin, constitutively produces this small molecule 6 n-hydroxy amino purine, a molecule that then inhibits DNA polymerase activity of both bacteria and some human tumors, suggesting a new rule for skin commensal bacteria in defending us from environmental assault from things like ultraviolet radiation and skin cancer.

So here’s the story. These authors went on a prospecting trip and in the course of testing strains of coag negative Staph epi, they isolated, they were looking from skin isolates, clinical isolates, for antimicrobial activities. And these authors identified the strain, which is MO37, that secreted a bactericidal activity against group A streptococci, or they refer to it as the GAS organism, which is of course Streptococcus pyogenes, the causative agent of garden variety Strep throat.

What was remarkable about this antimicrobial activity that it was both heat stable, where a hundred degrees is their definition of heat stable, and protease insensitive, suggesting that this factor was not a protein. So this is like a heretical concept for antimicrobials from gram positives, which are traditionally small peptides, things along those lines. So they were really probably very much excited about this. And if you think about it, our skin in this remarkable and large organ comprising about two meters of our surface with all these diverse microbes. And so what we–

Elio: Wait a minute because I heard a morphology talk about this recently. If you look at the convolutions of the skin, all the folds, it’s the size of a football field stadium, a football field. It’s gigantic, it’s the largest surface of the body.

Michael: A football field?! I thought the lung was, but that’s only a tennis court. A football field is of course much bigger than a tennis court.

Elio: I don’t know how big it is but it is huge.

Michael: So they purified this low molecular weight molecule using HPLC and they were tracking the antimicrobial activity, and what they learned is they recovered about 7 milligrams from about six and a half liters of culture liquid. And they then tested the molecule and they show beautiful data showing a dose response curve and this molecule is extremely active, it will take out all bacteria at about 0.5 micrograms per mL. We’re not talking–it just obliterates everything from a control. They determine its molecular formula and learned that it was synthesized by the microbe itself and it was not a fermentation product or breakdown of components associated with the medium or normal metabolism. And they accomplish that via old time religion N15 isotopic labeling. And this thing looks like a derivative of adenine. It’s a purine compound and it has the chemical formula C5H5N5, oh and an oxygen, and it’s 6 N hydroxy amino purine that they continuously abbreviate as 6HAP.

Michele: Michael, if we could just pause here, I was able to talk to the first author Teru and he described that the purification and solving the structure of this molecule, which is amazing, was about a three or four year effort.

Michael: Whoa!

Michele: So the day that they were able to confirm this beautiful structure that is shown in Figure 1E was like a huge breakthrough, because as I’m sure Michael will tell us it then led to predictions about its action. And that work was done by one of their co-authors, Michael, where is his name–

Michael: Michael Otto.

Vincent: Michael Otto.

Michele: Yes, who is a distinguished professor at Scripps and continues to mine the ocean for bioactive molecules that could be used therapeutically.

Michael: And he has got a phenomenal laboratory out at Scripps, and he has lots of interesting antimicrobials that come out of the ocean, and his claim to fame is he is an expert at identifying these compounds via mass spectroscopy, and as Michele has told us, it is figure 1D and the spectra are just spectacular. And how they decipher this is really very elegant analytical chemistry.

Elio: And here I thought that mass spec was a piece of cake, all you needed was somebody who could do it. It’s amazing they could have such problems, I didn’t know that.

Michael: Three years is nothing to sneeze at, and they are not naive when it come to mass spec. This is something that they routinely do in the Otto lab and when I heard his talk last year at a meeting I was attending, I was just mesmerized by the brilliance of this group

Elio: Isn’t Otto in DNH?

Michele: This structure was solved by William Fenical who is a distinguished professor of oceanography.

Elio: He’s at Scripps oceanography.

Michael: Yes.

Michele: He is the director of their Center for Marine Biotechnology and Biomedicine, which captures it all.

Michael: Alright, so summing that piece up, they have a new potent antimicrobial that looks like adenine, 6 N hydroxy amino purine. It is constitutively synthesized by this coagulase negative Staph epi. Now given the structural similarity of 6HAP to adenine, they then ask the next obvious question. Was DNA synthesis the target of its antimicrobial properties? And they did this really cleverly. They made a primer template and a fluorescent template. And they just used good old enzyme Klenow that I don’t think anybody under the age of 45 has ever heard of because it’s old, it’s one of the older DNA polymerases. Everybody today uses Taq. But Klenow is good for this sort of reaction.

The principal is that you have a primer and a template and since it looks like adenine, you know that as the extension reaction would extend, if it tries to put an adenine in in the presence of this compound it wont be able to do it because the compound wont be able to base pair with the template strand, and that consequence is you won’t get a product. And that is what they showed us, is that in DNA extension occurred normally when the template required a cytosine for extension, where the primer was a G, but as you might expect was blocked when the adenosine was required when the primer was a T. And so the net consequences, they show this beautiful gel where you just look at the primer and it glows in the dark, and you look for the extension product which they just show on an agarose gel, they just shine a UV light on it, and its a beautiful minus plus minus plus minus, and where they add the 6HAP, they don’t get the extension product.

So it directly inhibits DNA synthesis by interfering with adenosine thymine base pairing. So now, this is where it gets interesting. They next ask whether or not this compound could inhibit the incorporation of 5 bromo 2 deoxyuridine, or BRDU, which is the standard way you look for a tumor growth, and they as whether or not you would get incorporation of BRDU into tumor cell lines. And as you might expect, it did, leading them to conclude that what was isolated as a promising antimicrobial now exerts, and this was the beauty of the system, selective antiprolifative activity against several tumor cell lines.

And the key here to the series of experiments that they did was that it was selective in that the 6HAP did not inhibit the proliferation of primary keratinocytes, which those of you that remember your human anatomy, is the principal cell of our epidermis, our self renewing tissue that we generically refer to as skin. So again, Staph epi is our friend, and if you make the jump, which is how they spend the remainder of the paper, addressing whether or not this new antimicrobial has the potential as an anti-cancer med or more importantly routinely serves as a natural defense product for us from the effects of ultraviolet mediated tissue damage, or skin cancer.

Vincent: Michael, any idea why it is selective for tumor cells?

Michael: That’s the next experiment. And so they were, just like Vincent, they were very curious as to why 6HAP did not inhibit keratinocytes. So they asked a number of questions, whether it was about selective penetration, did the cells consume the material thereby inactivating the 6HAP whether or not it got in, and that is one of their more detailed experiments, which was effectively the series of panels associated with Figure 2. But the punchline is the expression of a mitochondrial amidoximes reducing component which are two gene products was much higher in primary cultured skin cells than that activity in cancer cell lines. And the cancer cell lines all were sensitive to 6HAP, but the primary skin cells effectively because of the amidoxime reducing components were effectively rendering the 6HAP inactive. So the keratinocytes have been adapted or selected in concert with 6HAP in this commensal relationship with Staph epi in order to effectively protect the keratinocyte from the effects of 6HAP, and you see that it actually inhibits the cancer cells but does not inhibit the ability of the skin to renew itself.

Michele: I was going to say, our skin cells can detoxify this microbial product.

Michael: Yes.

Vincent: Yes basically.

Michael: That’s the take home.

Vincent: But it’s also protecting, right, because if the host dies of a skin tumor the bacteria has nowhere to live. So you can imagine that being selected for also.

Michele: Right.

Vincent: The question I have is, this is like a protection against UV light, right? Now we know that skin color also is a protector, right? So I wonder if people who have dark skin and that is their protective mechanism, whether they have these strains of bacteria.

Michael: That’s effectively their last figure and they didn’t go into as much detail as to segregating it by race or skin color to effectively get at that particular question. But their next questions are asking whether or not 6HAP could selectively suppress melanoma. And they answer this question via a mouse model, and they ask the usual questions that most cancer biologists usually ask about a new promising anticancer drug. First is, was it toxic? Which they assessed in mice by systemic administration of repeated intravenous injections of 6HAP at the maximal soluble dose of 20 mgs per kg every 48 hours to the mouse for two weeks. And this resulted in no apparent systemic toxic effect. Anyone who has ever known someone who is undergoing cancer chemotherapy knows that the compounds out there are wicked to the people taking them, so this is actually great news.

And then the second question they ask is, did it control melanoma? And so they inoculated the mice with a rapidly growing isogenic melanoma cell line and they learned that the tumor size of this aggressive tumor cell line was suppressed by greater than 60%, and they show this beautifully, you just look at their figure on the back of this mouse and you see, you can literally see with your naked eye in this very small picture how well 6HAP is doing.

Now, they are good microbiologists so this is where they take us back to the microbiology, and here the authors ask whether or not the Staph epi strain producing the 6HAP could suppress UV induced skin tumors in mice. And they used again a mouse model, they use a 2 stage ultraviolet UC carcinogenic model, it has been well established in this SKH1 hairless mice, and they are treated with a very potent carcinogen first, a 7 12 dimethyl benzanthrocene, which is effectively tar, for about one week, followed by UVB radiation twice a week.

The mice were colonized by topical application of either a strain of Staph epi that produced this molecule or equal amounts of Staph epi that did not. They applied it at a concentration density similar to the concentration of Staph epi seen on human skin. So the mice with the control strain of coag negative Staph epi had the expected high incidence of tumor formation, again they show us the back of the mouse, you see the tumors while those that were colonized with the strain of Staph epi producing this low molecular weight compound 6HAP had a significantly decreased incidence and number of tumors.

When they looked at the histopathology of the tumors, they learned that 81 of the tumors in the 19 control mice identified as squamous papilloma, so that’s the gold standard of the model is indeed doing what they expected, and that the microscopic evidence also confirmed that papilloma formation was absent in the normal appearing skin of mice that received the inoculation of this Staph epi strain producing 6HAP.

Michele: That is such an amazing result. Wow.

Michael: The pathology, even I can see. I mean, you look, it’s really simple to tell. The pathology is so gross in their figure you can just take one look at it and say this is not like the other, which is effectively the gold standard for pathologists. They say this, you don’t want any judgment calls. So this enabled them to conclude that the strain of Staph epi producing this 6 amino purine suppressed UV induced skin tumors in mice, and their final question that Vincent got to earlier was whether or not the Staph epi strains producing 6HAP are commonly associated with human skin. And they went and they asked the question, do clinical isolates produce 6HAP, and they do indeed but the reference strains from the American Type Culture Collection or ATTC did not, nor did the control strain they used for their UV tumor model. So then they explored the likelihood of 6HAP being associated with human commensals. They used whole genome sequencing of the strain that they isolated, MO34, and analyzed existing metagenomic data sets of the human skin microbiome and strains producing this molecule were found, leading to conclude that Staph epi strains producing 6HAP are commonly associated with human skin.

Michele: That’s great news.

Michael: And proactively, these finding suggest a new role for skin commensals in host defense against environmentally mediated bad eggs. And overall this paper reinforces the importance, if you pardon the pun, that our second skin or microbiome is indeed protecting us from harm that we may not even know about simply from going out in the sun.

Vincent: Maybe people who get skin cancer are missing this or have different strains.

Michele: Or they’re too clean

Vincent: and Michael: They’re too clean!

Michele: They’re too fastidious.

Vincent: Michael, we should start slathering on the Staph epi, right, before we go to the beach?

Michael: You wonder, you’ve heard about probiotic tablets that we can take to enhance our gut, I’m wondering if they are gonna come out with a probiotic ointment that you can apply to sun creams in addition to the zinc oxides that they use to absorb the ultraviolet energy.

Vincent: You just need 6HAP in the ointment right?

Michael: You just need 6 amino purine, yeah.

Michele: That’s an option. I had a great conversation with our first author, Teru Nakatsuji.

Vincent: Nakatsuji.

Michele: Nakatsuji. He is an associate project scientist in the Gallo group and he is a co PI with Gallo on a NIH grant on this topic. He grew up in rural Japan in an area known as Mino which is about 20 kilometers north of Osaka. And he said that the outdoors were his playground, he loved to dissect frogs and fish, so he always wanted to be a biologist. In fact, his parents are still in that area, they are rice farmers, and he will be going back next month to help his parents with the next planting.

But anyway, this love of dissection and being out in nature served him well as a PhD student. He was using the American crayfish as a model system to identify bioactive components. So in particular he dissected, he collected 10,000 eyes from crayfish and used that to purify a hormone that then he learned is able to inhibit molting by the crayfish. So he does have really a classic training in biochemistry and purification. So that was why he is the lead on this paper. And he currently is now taking the lead on their clinical trials, Michael, as you pointed out, they are in the department of dermatology so they have got some physicians around that are collaborating with this and they are looking to see that, are these strains safe for people? Which certainly the screen that they did and found some 80% of people are colonized with Staph epi, we have every reason to believe this is going to be safe.

But they are interested in using this as a probiotic and in fact, he made the case that I thought was really interesting. Rather than use the molecule itself, why not include in your preparations the live bacterium, because many microbes produce multiple antimicrobials and so it would be like adding multiple antibiotics to treat a particular infection. You thereby reduce the risk of resistance. So they are excited about the possibility of a probiotic sunscreen and actually this group has published similar strategies in the past, they have shown that there are certain coag negative strains of Staph epi that can in experiments reduce the inflammation that is characteristic of eczema and they also are in phase 2 clinical trails for a similar probiotic treatment of acne, so probiotic bacterium acne is what causes most of the pathology in acne and certain of their strains are active against that in quashing that bacterial colonization.

Michael: That would be so much better than tetracycline.

Michele: Oh, yeah. And so he, when we were just talking about his career and the field and how exciting this was he said that when he first started this field, the people studying the microbiome of the gut were the ones in the headlines, they were making great progress, and the skin was really lagging behind. But in fairly short order they now have got really great animal models showing efficacy and now up to phase 2 trials for some of these probiotic skin treatments. So this is a really exciting area and he encouraged many junior scientists to consider pursuing this as a field.

Michael: The last figure 4 of the manuscript census is open source, the audience will be able to take a look at this, is really an outline of how they really took this and can actually bring this to market and the fluorescent images that they show in panel G and panel H just looking at the Staph epi that produce the compound on the back of these mice is actually very elegant how it just fluoresces and when you just look immediately above those fluorescent images you see the tumors on the back of that mouse. And you just sit back and you say to yourself, wow. It is just incredible that this little bacterium–

Elio: The thing that I find incredible about this paper is normally you discover something, you discover a phenomenon in this case the antibacterial has anti cancer activity of this bug, and then it takes a while you develop a mode of action, but here they have both in one, so they not only discover the phenomenon but they also explain it. And this is amazing.

Michael: It’s rare in today’s science.

Elio: It took time but they held off until they knew the whole picture. And it’s remarkable, I never see that.

Michele: It’s quite wonderful.

Elio: You can go to press with just the phenomenon.

Michael: The antimicrobial activity, or the anti tumor compounds.

Elio: And here they waited until they had the whole story and it took them years. So it is sort of amazing.

Michele: It is and even doing that final figure looking on what did they take, 18 healthy subjects and did a screen of different body sites, more than a dozen different body sites and just asked how common do you find this strain that produces 6HAP, and happily they find it very common, happily hah, that’s a pun.

Vincent: (laughs)

Michael: (laughs) It is.

Michele: Happily they find 6 HAP in many different sites in many people. So.

Elio: That’s right.

Vincent: It’s really amazing, yeah. It’s a great paper and look forward to hearing what happens in people.

Elio: It’s also the yin and yang of bacteria, right?

Michael: Yes.

Elio: Bacteria are supposed to do bad things, here bacteria are doing good things, and many other instances of course. To us it is very familiar, but it is not familiar to the general public that there is a possibility of using bacteria for really very useful things in medicine.

Vincent: Michael, one last question, so this is also an antimicrobial, right? So it does not inhibit itself obviously. What about other skin commensals?

Michael: It went after group A strep, and that was what they were characterizing in the first component of their figure. They are just doing simple diffusion assays and they literally show that it is inhibitory to group A strep, which is a frank pathogen that every parent is fretting over because of the rheumatic consequences associated with group A strep.

Vincent: What about other commensals that are not pathogens?

Michele: Even Staph aureus is sensitive, so that is really interesting.

Vincent: But there are other commensals on our skin that are beneficial, right, Michael?

Michael: Yes.

Vincent: They must not be inhibited by this.

Michael: And that’s probably the original natural selection is to enable Staph epi to have a niche on the skin because it is not traditional moist. It’s a limited way of diffusing so it can set up those good fences or good boundaries so it can effectively live.

Vincent: Very nice, thank you Michael.

Michael: You’re welcome.

Vincent: We have here a lovely photograph of art produced by, sent by Mark Martin. I believe his wife actually made it, which is an image of Elio.

Elio: Thanks.

Michele: Yeah.

Vincent: It’s beautiful, really nice.

Elio: It is nice.

Vincent: So these are fluorescent bacteria, is that right?

Elio: I’m a little bit embarrassed, but it’s okay.

Vincent: Well, it looks like you.

Michael: It looks like you!

Elio: It does look like me and I find it very expressive.

Vincent: It is! It’s quite nice.

Michele: It’s really great. And can I just say, Mark Martin has been such a great advocate and proponent of microbiology. He takes this agar art show on the road and has done sessions at regional meetings but also at our national meeting where people can create their own art with this strain of bacteria. So hats off to Mark.

Vincent: They’re bio-luminescent, right?

Michele: Yes.

Michael: It’s Photobacterium leiognathi, and I found a reference in the journal of bacteriology that specifically describes how this organism makes its light, so if you are interested in learning the nuts and bolts, Ray will put that in the show notes so you can see how these organisms glow in the dark.

Elio: Is this strain better at making light? Does it make more light?

Michael: I don’t know, it seems to be making quite a bit of light.

Elio: Right, I was wondering whether–

Michele: I think it’s also figured out how to culture it, too, to maximize the production of light.

Elio: That’s probably right. Now, I really, the amount that the skill involved in this kind of stuff is absolutely remarkable. Mark’s wife must really be, she’s a mathematician by the way, but she must have picked up the skill of making art this way in spades. It’s just amazing, I can’t quite believe it, I can’t quite picture how she does it.

Michele: It’s a great partnership.

Michael: It gives a whole new meaning to the word watercolors.

Vincent: (laughs)

Elio: (laughs)

Michele: So Mark is going to be honored this year as the Carski winner which is given to somebody who has made a huge impact on microbial education in microbial sciences so he will be making an award presentation both at ASM and ASM CUE which is the educators annual meeting. So if you are interested, check it out.

Vincent: Nice. Alright, a couple of emails. First one is from Sarah.

Hello, I have been listening to TWIM on and off for a while now, but still can’t figure out how I can enter into drawing for book giveaways. Are you able to provide me a link to such entry or steps I might take in order to be eligible? I am a current ASM student member.

Well, Sarah! The only way you can win a book is to listen to TWIM and listen to when we announce it.

Michael: And then send a letter, send an email.

Vincent: And it just so happens, Sarah, that I am going to give away a book right now, and it is called Clinical Laboratory Management. It is the second edition, the editor in chief is Lynne Garcia, and this is a huge book published by ASM Press all about managing clinical laboratories, principles of management, economic and business functions, managerial leadership, personnel management, requirements for effective management, financial management, revenue generation, profitability, marketing, expansion, and then, of course, they go into some science, all the tests and so forth. But this is really unique and I certainly don’t have any use for it.

Michele: (laughs)

Vincent: So I’m going to give it away to a randomly chosen email sent by a TWIM listener, you have to send an email, Sarah, to twim@microbe.tvand the subject line, this is very important, has to be “micromanagement”. Get it? It’s a little joke. Micromanagement. Again, send an email to twim@microbe.tvsubject line micromanagement and we will pick a number out of the hat and see who wins. Michael, can you take the next one from Dallas?

Michael: I will!

To the masters of the microbiological universe, your discussion of a hyperthermophilic bacterium that produces hydrogen was very interesting and a lot closer to my background than most discussions. The production of hydrogen by anaerobic fermentation is a very common process and occurs everywhere from a cow’s gut to landfills. My understanding is that the bacteria that initially break down polysaccharides like cellulose producing hydrogen, CO2, and acetate or lactate and other short chain fatty acids, within the cow using acetate for energy with the hydrogen becoming a waste product. However, like most energetic margin chemical reactions, a buildup of waste products inhibits the reaction rates, Le Chatelier’s principle from chemistry class. So the hydrogen concentration needs to be reduced. That is where the archaeal methanogens come in that obtain their energy from a small amount of free energy available from producing methane from hydrogen and CO2 that is the greenhouse gas from cattle and all ruminants. And landfills along with hydrogen and CO2 producing methanogens you also have methanogens that convert acetate to methane that keeps the pH from dropping.

Methanogenic archea tend to be very pH sensitive, so if the pH drops in an anaerobic fermentation, your methane production stops and you end up with hydrogen in the gas at high enough concentrations to inhibit the initial fermentation of the carbohydrates and everything shuts down. Having your anaerobic bioreactor in a sewage plant go sour is a problem. When preserving silage for winter cattle feed, you don’t want all your carbohydrates turned into methane and lost to the atmosphere. Having acetate bulid up and sour the mix is thus good. The genius of man figured out this fermentation pH CO2 hydrogen game long time ago, with all the ways to preserve foods like cabbage for winter. From a production bioreactor viewpoint, using hyperthermophilic bacteria and other extremophiles for doing your environmental chemistry makes it easy to maintain biosecurity in an open system.

The bacteria in the discussed paper were way too hot for most containment species that would turn all that hydrogen and CO2 into methane, and their electromotive potential or EH was a bit high for many methanogens. Being hyperthermophilic could allow defined species productions of a single cell protein and lactate for the animal feeds market, and not have to worry about contamination from some of the real nasty bacteria like Clostroidium botulinum. Many of the excellent papers in this area are from diverse countries around the world. Good science is good science wherever it is produced.

And that’s from Dallas.

P.S. Sorry about being behind in my listening. And he’s at the Scientific Hatcheries in Huntington Beach, California.

Vincent: No problem in being behind, Dallas, thanks for the great email. (laughs)

Elio: It is, my God.

Vincent: Really good stuff. We have some erudite listeners.

Michael: Yes.

Elio: Wonderful.

Vincent: Michele, are you able to read–I’m sorry, you want to say something, Michael?

Michael: I was just gonna say the next email is, it just warmed my heart.

Vincent: Michele, can you read that, or are you?

Michele: I sure can.

Hello TWIM listeners. My name is Cherish Hughey. I am a fourth grade teacher at Riverside Prep elementary in Rural Grande, California, a really small town along Route 66. My students currently completed a science project that I want to share with you. After learning about microorganisms, the students were curious where the most germs could be found around our school. So the students picked 5 places to test, a tether ball, playground equipment, a chair in the nurse’s office, the music room mats that they sit on, and the keyboards in the computer lab. Samples were wiped on agar plates and the wait began. After a week, the students were totally grossed out that the music rooms mat they sat on had the most growth on their agar plates. The students have now requested that the music room mats be replaced or cleaned regularly as a result of their findings. We are still waiting for the principal’s answer. (laughs) I am trying to inspire future scientists. I hope you enjoyed their project. I love the show and look forward to listening on my daily commute to school. Have a great day, Cherish Hughey.

Vincent: That’s wonderful.

Michele: So now I’m wondering if the music room mats might have had coagulase negative Staph epidermidis and the children or students might prefer to actually roll around on those mats rather than have them sterilized.

Vincent: So she included some photos of a poster that they made, and the plates.

Michele: That’s great.

Vincent: Michael, or whoever, do you know what kind of plates these are? They’re white.

Michael: They just look like nutrient agar plates or maybe potato starch plates.

Vincent: Potato starch probably, right.

Michael: Yeah, something that you can get from Carolina Biologicals that will grow.

Vincent: Different colored organisms, right.

Michael: They are indeed. She has a closeup shot and it’s absolutely brilliant and they’re skin organisms though, the bright orange ones are probably Corynnebactera that are also normally affiliated with our skin and the pigmented bacteria of course fall off of us all the time, so. They are truly discovering what’s coming off of them, the human, we shed a lot of skin each day, and they’re accumulating on those music room mats.

Vincent: This is great because they get to see, they do the experiment, they get to see what’s on them, it’s a real life thing and it’s relevant, right. So that is why this is great, Cherish, I think this is so cool. Keep it up.

Michael: The next experiment is to ask whether or not they wash their hands before lunch after seeing this experiment and I’ll betcha seeing how may bacteria are associated with the music room mats, more and more of those children will be going to the washroom and washing their hands before they eat.

Michele: Always a good practice.

Michael: Always a good practice.

Vincent: To the students in Miss Hughey’s class, great job and you made it to TWIM. (laughs)

Michael: You made it to TWIM.

Michele: Great poster, too, with the hypothesis, the experiment, the research, the data, the conclusion.

Vincent: Great job. Alright, don’t forget book giveaway, Clinical Laboratory Management, send us an email twim@microbe.tvwith the subject line Micromanagement. Of course you can always send us questions, comments, you can send us your school projects too, we’d love to get them and put them up there on the TWIM website. If you like what we do, consider contributing. You can go to to find out how. On today’s TWIM, Michele Swanson from the University of Michigan. Thanks, Michele.

Michele: Thank you.

Vincent: Elio Schaecter form Small Things Considered, thanks Elio.

Elio: My pleasure. I enjoyed it.

Vincent: The humongousest blog, right?

Michael: (laughs) With the name Small.

Elio: Humongonest fungest.

Vincent: Michael Schmidt is at the Medical University of South Carolina, thank you Michael.

Michael: Thank you, everyone.

Vincent: I’m Vincent Racaniello, you can find me at Thanks to ASM for their support of TWIM, Ray Ortega for his technical help, and Ronald Jenkees for his music. 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.