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TWiM 112 Letters

Steve writes:

Mysterious fungus killing snakes in NY, at least 8 other states | wivb.com - http://wivb.com/2015/08/10/mysterious-fungus-killing-snakes-in-ny-at-least-8-other-states/

One for Elio, if he's not on to it already.

Amphibians, bats, and now snakes: have the fungi just declared war, or what?

All the best,


Petra writes:

Dear TWiM,
Thank you for your excellent discussion about graduate and postdoctoral education in TWiM 108. I enjoyed the conversation about career options for people with advanced training in microbiology. I earned my PhD in microbiology and did postdoctoral training before taking my current position as a research scientist at 3M Company. As a scientist doing research in industry, I don't think of my career path as "alternative", although I often hear that term used to describe non-tenure track careers for scientists. It would be a step in the right direction for advisors in graduate programs to start using the term "careers" instead of "alternative careers" when talking to students about options for the future. The use of the word "alternative" to describe non-tenure track career options seems to be particularly pervasive in academic departments specializing in the biological sciences. As biologists, let's start a movement to catch up to our colleagues in chemistry and physics departments where moving to non-tenure track positions after graduate school is a normal and valued option.
Many thanks for a great show. Listening to TWiM is a great way for me to stay current on a wide variety of topics in microbiology, which is not only fun but also part of my job.

Anthony writes:


Suzanne writes:

I was so confused when I first heard you talking about this. It sounded so familiar I was sure you'd mentioned it before but it sounded like it was new to you. After a bit of thought I wondered if I'd heard of it during a class I took on Beowulf last spring. I checked the discussion board archive and there it was! Someone had linked to an article about it on newscientist.com. What a cool overlap between online communities! If you're still wondering, the language spoken in England back then is now either called Old English or Anglo-Saxon. Beowulf was written in that version of English and it's nearly unintelligible today unless you spend time learning the language. But there are still familiar words here and there. Chaucer wrote in Middle English which we English speakers can still understand somewhat without a whole lot of help. My favorite thing about Old English, really about pre-printing press English, is that there were dedicated letters for our "th" sounds. One was like a cross between lower case p and b which looked kind of like a mouth with a tongue sticking out. Which makes perfect sense.

Wytamma writes:

Dear TWiM Hosts,

My Name is Wytamma, I am a honours student in microbiology studying in North-Eastern Australia where it feels like a pleasant 18C. FYI honours is a year of postgrad research that can bridge you into a PHD without completing a masters degree. Anyway, my question is about Taq polymerase. My girlfriend Anna is currently doing some TA cloning and I was surprised to hear that the Taq pol enzyme adds an adenine overhang to the ends of the PCR product making it perfect for this cloning method. I was wondering what biological significance this function has? I guess the the first step would be to insert a polymerase lacking this function into the bacteria and seeing what happens but I’m a little busy with my own project on ranavirus to take that on.

Thanks for the great podcasts,

All the best,

James Cook University
College of Public Health, Medical and Veterinary Sciences
Townsville, Australia.

[this is a property of many DNA polymerases, adding a single non-tempated nucleotide to the 3’-end of a blunt strand. Function unknown, as these polymerases copy circular DNA genomes. Perhaps it is a signal of DNA damage?]

Matt writes:

Hi Twi Team,

Absolutely love your podcasts. I’m a public health specialist coming to the hard sciences late in life and enjoying it immensely. Thank you for all you do communicating the wonder of science.

That said… I think you blew it on the public good explanation in TWiM #111.

The reason public goods are fundamentally different than private goods is that unlike with private goods, the producer of the public good gains no advantage vis a vis his peers. If a Pseudomonas bacterium developed a mutation that allowed its siderophores to differentiate gallium from iron, that benefit would be diluted across the entire population of the colony. Everyone - including the mutant - would encounter the same environment filled with a majority of gallium-bound (and therefore toxic) siderophores. There would be no individual survival advantage to the individual that developed the mutation - thus no selection pressure.

Now if there was a mutation that allowed a cell to make use of the gallium as if it were iron in its cell processes, that would be a different story since that would be an individual advantage and would be selected for. But given the diversity of uses of iron in various metabolic pathways, the likelihood of an individual mutating to accept gallium in all the places where iron is currently used is essentially nonexistent.

So public vs. private does matter.

Keep up the amazing podcasts. My dog loves your show because he knows when I put on the headphones he’s going for a long walk!

Peter writes:

Dear Twimers!

I'm Peter, writing from Falmouth, UK (not to be confused with it's no-doubt sunnier namesake in MA).  We're somewhere about 16˚C (that's about 61 in your currency), with showers, and autumn is starting to tell.

I'm just writing to comment on the evolution of resistance to public-goods based antimicrobials  - the gallium storey in TWiM 111.

I'm going to first run with the assumption that there is a mutation somewhere in gene space that allows a siderophore to exclusively pick-up iron.  Then the problem with public-goods (for the bacteria, that is), is that the individual bacterium that gets that mutation isn't necessarily the one that gets the fitness benefit from it:  It's highly likely that the super-siderophore gets taken-up by a different bacterium, as the siderophore diffuses away from the bacteria that produced it, and then the fitness advantage is conferred on an individual who didn't have that mutation.  I guess that the selective advantage for a super-siderophore will be higher in a more viscous media; one in which the siderophore remains spatially close to the bacterium that produced it.  

I suppose most of the places we're going to be medically concerned about P. aeruginosa are going to be places with a bit of spatial structure, but still the fact remains that compared to a completely "privately operating" mechanism, a "public goods" based anti-microbial will be less prone to resistance, simply due to the "who gets the benefit of the mutation" idea, though it seems to me that resistance would none-the-less eventually evolve given sufficient time and selective pressure.

That's all, except I just want to say that I have a lot of love TWiM and TWiV and what you guys do; over the last 5 years of tuning-in you feel like familiar characters, the sort that I might regularly meet in the local pub and chat the night away with.   And as a PhD student who never does enough reading I cannot say enough what an amazingly useful tool you guys are providing: multiple lifetimes-worth experience pouring over the latest, bleeding edge research with such wonderful insight.  What an inspiration!

Cheers all, and here's looking forward to 112 and beyond!

Kevin writes:

Dear Twimmers,

I am writing to help clear up some confusion as to why resistance might be hard to evolve if public goods are targeted.

In episode #111, Elio talked about gallium intoxication of siderophores, and a proposal was put forth that since the siderophore is extracellular, it would be hard to evolve resistance to gallium.

Vincent said, it is the atomic mimicry of gallium and iron being so similar that is important: loss of gallium binding would almost certainly cause loss of binding to Iron.

Elio replied that both the extracellular nature and the mimicry are important, but why extracellular matters was perhaps not so clear.

I think the distinction is not extracellular vs. intracellular, but rather that the siderophore is a public good, that has impacts on a population of bacteria. In contrast, mutations that may produce an altered siderophore occur in individual bacteria.

What this means, is that mutant bacteria bacteria that produce a siderophore that distinguishes iron from gallium does not receive the full fitness benefit of that mutation. Instead, the whole population of surrounding bacteria will receive that benefit.  In this manner, fitness advantages from a mutant are redistributed to a community, instead of benefiting only the mutant bacterium.

However, in my opinion, this is still not necessarily a satisfactory explanation as to why resistance would not develop. Even if the whole population receives the advantage from one individual, the mutant bacterium is among that benefited population and will receive some benefit.  The counter argument would be that by spreading the fitness advantage among a population, the fitness advantage is so diluted that there is virtually no selective advantage conferred to the mutant bacterium. Personally, I think targeting public goods such as a siderophore may slow expansion of resistant alleles in a population, but not prevent them from occurring.

It's interesting to conjecture that diffusion properties of these "public goods" (to a large population or a relatively small population of bacteria) may impact the rate at which natural selection occurs.

Thanks for your great work, look forward to the next episode!

Postdoctoral Fellow Brigham and Women's Hospital


TWiM 111 Letters

Noah writes:

Dear Dr. Schaechter,

First off, I want to thank you for the effort you and your colleagues have invested in Small Things Considered and the podcast TWIM.  Back when I had a longer commute to work, I listened more religiously than now, which is pretty much the only thing I regret about switching my job and reducing my commute.  As a physicist, turned synthetic biologist, I really need an education in microbiology (that most of my peers got in graduate school), and TWIM is a great resource for people like me.

Now, a question:  (I apologize if this topic has already been covered by you in a previous post or article.)  Thermophilic organisms have DNA sequences that are higher in GC content in order to remain stable at higher temperatures.  The enzymes and protein structures found in thermophiles are also significantly more thermostable.  If you were to examine a conserved enzyme from psychrophile through the temperate zone and up to thermophile, what do you see in terms of its amino acid content?  Are there certain amino acids that are correlated with thermodynamic stability of the protein (fold)?  Do these amino acids correlate with higher GC codons?  If so, do you believe that this was part of the driving force for the evolution of the genetic code?  Namely, that a more thermostable codon should correspond to an amino acid that is more likely to contribute to a more thermostable folded protein.  (This thought never occurred to me before, but I read the abstract of this paper (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403753/) and it seemed to imply this concept, which struck me as sensible, but I hadn't heard it before.)

Thanks, in advance, for any thoughts and for your time to help educate us all,


Christoph Weigel responds:

hi noah,
in principle, your ideas are fine. yes, GC-rich DNA has higher melting temps., GC-rich genomes - as e.g. streptomycetes - tend to have a bias towards G and C at the 3rd position of codons in their genes, and also more G and C in conserved transcription factor binding sites. however, there's a big caveat: one of the most thermophilic bugs we know today,
the archaeon pyrococcus furiosus (grows at 100°C, has a wikipedia entry), has a genomic GC-content of 40% (see here: http://www2.unil.ch/comparativegenometrics/AE009950.htm) that's 10 points less than e. coli. if i remember correctly, there is evidence that this bug employs histone-like proteins to keep its DNA double-stranded. and given it's low genomic GC-content it can't have this codon bias. i could/would go into more detail - if you want - but not before end of september as i'm on vacation right now, enjoying açores islands :)

then Noah responded:

Hi, and thank you for your quick response from your vacation.  (Do not feel that you have to respond again before returning!)  

I guess my question was not "do all microbes that live at higher temperatures also have higher GC-content genomes?" since that is easy to disprove, as you pointed out... Instead, I am wondering about the evolution of the genetic code and the transition from a RNA-world to a protein-world: At this moment in evolutionary history, was thermodynamic stability a driving force of the genetic code?  I am assuming that an early RNA-only ancestor of modern life (all of which has protein enzymes, correct?) would very likely have needed ribozymes that were stable at its ambient temperature, and thus, higher in GC content.  Also, we should be able to determine (using bioinformatics) if microorganisms that survive at higher temperatures have a consistent skew in the amino acid content of their proteins.  For example, if these thermophiles had a disproportionate number of Gly (GGN), Ala (GCN), Pro (CCN), Arg (CGN), then you might be curious about whether thermodynamics were a factor.  Looking a little more deeply, you could also ask whether individual transitions from similar amino acids (such as Lys to Arg) contribute to stable folds, since they are also more stable codons (e.g. a comparison between AAA and AGA).

I think it's probably clear that this will not account for everything, but just wondering whether anyone else had thought it may have been a factor.  Are there any papers considered "seminal" in the field of the evolution of the genetic code?

Thanks again for your time!  Cheers and enjoy the rest of the summer!


Veronica writes:

Hi all,

I was quite excited by your podcast on AMPs since I studied bacteriocin usage in bacterial vaginosis (BV) prophylaxis as part of masters. So in response, bacteriocins have been identified that inhibit BV-associated pathogens while having little impact on normal microflora in laboratory environments. There's been some promising research on bacteriocin usage but it's been most extensive in food research. Finally, a self plug for a recent publication: I just wrote a review on bacteriocins and their potential usage in conjunction with antibiotics which is currently in press in IJAA.

I love the podcast so much!


Andrea writes:

Hi  TWIMitos!

Have you seen this? Unbelievable!


It is 64F and "rainless" in Seattle.

Love the podcasts.


Will writes:

Love the podcasts, keep them coming! In response to Michele bringing up the NYC Legionella outbreak Vincent was trying to come up with Michigan-specific infections. Unfortunately, here in Southeast Michigan (mostly in Detroit) we seem to have created a breeding ground for infections with highly resistant organisms including CRE, VRSA, healthcare-associated Acinetobacter, and even a "small" outbreak of 5 cases of colistin-resistant, carbapenem-restistant Klebsiella. (http://aac.asm.org/content/55/2/593). Some have suggested this is due to the high prevalence of diabetes, end-stage renal disease, as well as high baseline rates of MRSA and VRE infections in the area. All of these factors increase the probability that a patient will at some point require vancomycin or a carbapenem to treat an infection. So apparently multidrug-resistant organisms are Michigan's microbial gifts to the world. Anyway, as a medical student I don't get a ton of time to enjoy our wonder summer weather (27°C today) so I'm going to go do that while it lasts.


Don writes:

Pages 41 to 45 of Popular Science magazine, Aug 2015 discusses the danger of our war on bacteria and viruses. They cite hospitals problems where 75000 people die of hospital acquired infections in spite of strong efforts to make things sterile. This war may be related to the rise of the superbug that is rendering our antibiotics useless. The space Station is probably a dangerous place because of the lack of normal microbes.

Brian writes:


This article in the most recent issue of Scientific American (special issue with a picture of Einstein on the cover) reminded me of the points you raised during a recent episode of TWiM.  

It has long been my opinion that the best advice to give to someone in school is to develop expertise in two complementary fields.  In my case I was able to combine skills in shipboard engineering and maintenance with at least a modicum of understanding of computer technology.  Similarly, I think that someone with a degree in microbiology who is fluent in Portuguese (the Brazilian variant) or Chinese would be in a strong position.  A person with a degree in microbiology who went to law school and specialized in intellectual property law could probably retire at 40.  

The attached article describes a need for a marriage between computer scientists and neuroscientists (and by extension with any of the biological sciences).  That marriage sounds like a promising “combination” for a student — a major in microbiology and a minor in computer science, or vice versa.  


TWiM 110 Letters

Trudy writes:

I'm sorry, I may have missed something, but the mechanism behind an effective vaccine is still unclear to me, since infection with F. tularensis does not confer protection. How would a vaccine work?

Katy Bosio replies:

In general, any protection against tularemia is very dependent upon the dose of secondary infection, the route of secondary infection and (likely) the subspecies of infection. Following infections with virulent subspecies, the evidence suggests that there is some minimal "protection" against low dose secondary infection. In humans this would be manifested as a very sick person, ie you might want to die, that had a delayed development of symptoms or someone with slightly attenuated symptoms. However, if the dose is modest to high it's unlikely that the small memory response one generated in the primary infection will be effective. Moreover, infection via inhalation poses its own problems, since the bacteria thrive within the pulmonary environment while evading a suppressing inflammatory responses- a critical element if one wants to jump start adaptive immunity.

Finally, if one is infected with a type B strain (the less virulent, but still pretty nasty) there is some, but not optimal protection against infection with fully virulent type A.

All of this is supported by evidence from human trials using an attenuated vaccine strain (LVS). This vaccine (which is no longer licensed in the US) was generated from type B FT and offered pretty good protection against low to moderate cutaneous infections. It also engendered some protection (in one study around 50-60%) against low doses of aerosolized FT. However, it was very poor at protecting against moderate (around >1000) doses of FT delivered by aerosol. Also, retrospective studies have indicated that people needed yearly "boosters" of LVS to protect against pneumonic tularemia. This supports the observation that long lived immunity against pneumonic tularemia is difficult to achieve.

We can recapitulate most of these findings in our animal model. So, what do we do? My lab has generated some immunologic tools to really dissect how vaccines protect against low doses of FT as well as how virulent FT modulates the innate, and sequentially adaptive, immune responses. By identifying what the host needs to survive on a molecular and antigen specific level we will be able to design a vaccine and vaccination strategy that gets the better of this bug.

Hope that's helpful and glad to hear that people took an interest in this incredible bug.

Julie writes:


Thought you would like to know that you have saved many lives in Houston -- when I listen to TWIM during my commute, I am not tempted to use my car as a weapon or a means to clean up the gene pool, I'm thinking too much.

I teach microbiology at a community college and use TWIM for ideas that I can use in class -- applications of the basic material we are covering, new information to update the textbook, etc. In a recent episode, you were talking about how important it is for students to do research to really understand science. We are incorporating that idea into several of our classes here: for the last two years I have had my General Micro students do research projects. The level of their questions has been amazing and their excitement is infectious (pun intended). Our biotech students also do research projects in some classes, but also take advantage of a "project lab" that is open to students to try out ideas -- it is equipped with equipment and some supplies for growing algae and bacteria, making biodiesel, prepping scanning EM samples, making microbial fuel cells, and testing samples for bioremediation. I am going to try to take this research approach to an introductory, non-majors class (I'm trying it with honors students first) by giving them choices of six different types of projects (bacterial pesticide degradation, DNA barcoding of algae in nutriceuticals ...) that have many different ways to go. They will get to work on projects that they "chose", so I hope the buy-in will be there. You will notice how many of these projects are based in microbiology -- great systems to use, little cost. Some of our projects are supported by NSF, others we just do because we can see the benefit for students. It was nice to hear that those of you at universities can see the benefit of what we are doing -- it may be easier for us to do because we can focus on teaching.

Thanks for all the mental stimulation,

Julie Harless, Ph.D.
Professor of Biology
Lone Star College Montgomery

Robin writes:

Anaerobic region of the mouth:
The buccal cavity does have an anaerobic region, the gingivodental sulcus. That is why anaerobes are less likely to be found in aspiration pneumonias in edontulous patients: they have no gingivodental sulci. Proper brushing addresses the buccal and palatal/lingual aspects of these sulci, while flossing takes care of the mesial and distal aspects.

Dennis writes:

Michael's discussion about tooth decay was very interesting and reminded me of a remarkable dental scientist and professor, Dr. Westin Price, who had discovered specific links between malnutrition and not only tooth decay but also to malformed arches and consequential sleep apnea. His book, "Nutrition and Physical Degeneration" was used in dental classes for two decades. A huge increase in tooth decay, sleep apnea, orthodontics necessary due to crowded arches, and more dental problems had ramped up by 1930. Turns out that a lot of it was due to a huge ramp in white flour and sugar, the flour having had all protein and micronutrients removed from it to make it purely white. So what does this have to do with Microbiology? Stay with me, it's coming. Price and his wife traveled the world during summers for a decade and compared the teeth and arches of each group of people. He compared groups living mostly isolated from the Western diet and those who lived in a town with access to white flour and sugar. The differentiated groups lived close to each other, just isolated by what today would be short car rides. The differentiation became clear: Western diet, high cavity rates, non-Western diet, very low cavity rates. Anyway, the Microbiome connection: he traveled in 1931 to a remote Swiss valley that was nine days walk from a town. He inspected the teeth of all of the kids in school. He found only one cavity in 600 teeth, similar to but lower than the ratio of other non-Western diet children. But in this valley, everyone's teeth were covered with a green slime. They didn't brush their teeth by the way. So I'm wondering if this is a clue to a microbiome that has teeth protecting properties. Is anyone in the listening community interested in trying to track down what this microbiome is/was? You can say or post my email address as This email address is being protected from spambots. You need JavaScript enabled to view it. . My pick of the week is his book which has experienced an increase in popularity due to its clear evidence and implications. It's $21 at amazon. Here's a link:http://www.amazon.com/Nutrition-Physical-Degeneration-Weston-Price/dp/0916764206

Keep up the great work. Gosh, the TWIx on Wolbachia controlling male/female moth ratios and the possibility of a phage vaccine was all incredibly fascinating. Best to all. You are changing lives.

TWiM 109 Letters

Geoffrey writes:

Dear Doctors:

I just went to my semi-annual dental appointment and I thought of a potentially interesting oral health monitor - the plaque biofilm that they scrape off your teeth during the cleaning. Brush immediately before the cleaning to remove the loose food bits then send the scraped-off plaque biofilm for sequence analysis. It wouldn't have to be deep-sequencing. It would only need to monitor the presence of, say, twenty common plaque microbes. Obviously, detection of dangerous pathogens would trigger a return visit but I am thinking that the plaque biofilm is probably a fairly stable and person-customized biome so any serious changes to the biome would trigger further dental investigation.

Do you folks have familiarity with dental plaques (or could you get a guest on)? What kind of sequencing testing might be effective and affordable for this kind of monitoring?

As always, I enjoy your show and my special thanks to Dr. Swanson for allowing a fan-boy to visit her back in April, I believe.

Mark writes:

Hello Current TWiM Cohort,

I’ve enjoyed your recent additions of talmudic questions into show episodes. I was surprised one of your listeners wrote in saying, and I paraphrase, that using the word “talmudic” was introducing unprovable theology into the show and veering away from science.

Growing up and studying on the East Coast I came to understand “talmudic”, with a lowercase initial ’t' as an adjective. Its meaning being roughly “the study and making specific distinctions between things relevant only to experts”. Written with a capital ’T’ the word becomes a noun meaning study or interpretation of the Jewish Torah. The word “catholic/Catholic” is also an adjective or noun depending on the case of the initial ‘c’ in the word. Spoken word podcasts don’t differentiate case, and can be ambiguous.

In a recent episodes there was discussion about the human immune system, its “memory” and “loss of memory” by B (or was it T?) cells. This anthropomorphizing raises several interesting, and — dare I say — talmudic questions. They are:

1. How did the human immune system evolve to have different memory ability for different pathogens?

2. How does the immune system lose memories? Isn’t the ability to recognize and fight non-self pathogens a benefit?

3. Is there a beneficial function by “memory loss”, i.e. the immune system losing memory about some pathogens?

4. Is immune system “memory loss” a result of pathogens that have a near homology to the self’s own proteins?

5. What is the essence of the immune system’s memory - is it the structure and shape of a pathogen’s proteins?

6. If spoken or written fiction creates human memories, then is there a corollary in terms of the immunity system?

7. Can we fabricate different shape proteins to create immune system memories against real or imagined pathogens?

8. Is the cytokine storm analogous to the immune system using “dumb” bombs instead of “precision laser-guided” munitions?

9. Is there an immune system corollary to PTSD, i.e.does it suffer dysfunction resulting from memories of past activities?

I offer these up as talmudic — small t — questions for you TWiM Hosts and your listeners. If any of these questions have answers, please explain and strike them from the list.

The journey is the reward.

Jim writes:
Hi All,

Heard this three part program from the Canadian Broadcasting Corp and thought it might be of interest:

Science Under Siege, P1 55 mins (165 mins total) - “Scientists around the world are increasingly restricted in what they can research, publish and say -- constrained by belief and ideology from all sides. What happens to societies which turn their backs on curiosity-driven research?” At the link find the title, “Science Under Siege, Part 1,” right-click “Media files ideas_20150603_33313.mp3” and select “Save Link As” from the pop-up menu. Do the same for P2 and P3 for their media files.

I've attached downsized versions of the files, but they may still be too big to get past my server's limits.


Jim, Smithfield, VA

Edward writes:

Hello TWIMers from State College, Pennsylvania. As most residents would agree, summer is what earns this place the name Happy Valley, with plenty of warm weather, lots of festivals, and plenty of options for outdoor recreation. This summer we also have had more rain than we know what to do with (sorry Elio).

I was driving to my sister and brother-in-law’s cabin outside of Syracuse this 4th of July, and my inner nerd was more than happy to make this drive a total TWIM-binge. Let’s just say I listened to many, many episodes. I was on Route 13, making the climb out of Ithaca, NY with a beautiful view of Cayuga Lake on the left, listening to episode #105, when Michael made this ASM Division P Chair smile with his food microbiology discussion about E. coli and Salmonella contamination on fresh herbs. That giddiness was short lived though, as he wrapped up the story saying he learned growing up “the old adage that you should eat local and not global”, implying that the globally-sourced herbs from this study were the reason behind the levels of contamination. Luckily I was past Cayuga Lake by this time, as I may have driven off the cliff that leads to it otherwise.

There are several reasons to eat local, including to support your local economy and its hard working farmers, and to eat produce that is as fresh and tasty as possible. Unfortunately, the myth that local means safer perpetuates in the minds of many people. My colleague Dr. Catherine Cutter and her talented graduate student Joshua Scheinberg, for example, highlight several outbreaks from small vendors selling strawberries, bagged peas, and cashew cheese, as well as known hazardous foods that are mistaken to be safe because they are local, such as raw milk (1). Cathy and Josh have also shown that chickens purchased from Pennsylvania farmers markets have a much higher incidence of Salmonella and Campylobacter than store bought chickens (2). To food microbiologists, this is not terribly surprising in retrospect, as the big “factory farms” have armies of microbiologists developing strong pathogen control programs, and these companies strive to ensure that their products a
re refrigerated continuously from the plant to wherever they end up across the United States. Unfortunately, many in the press spun this paper as implying chicken from farmers markets isn’t safe, when the more accurate conclusion stated in the paper was that these vendors need proper training to minimize risks to the purchaser. The smaller clientele base, limited distribution area, and CDC estimates that only one in 30 foodborne illnesses caused by high profile organisms such as E. coli, Campylobacter, and Salmonella get reported (3), means that the larger food producers and distributors give epidemiologists more data points to confidently identify an outbreak. This is a better explanation for why most foodborne outbreaks covered by the press are linked to larger companies.

You also correctly stated that washing produce reduces pathogen load (but doesn’t eliminate it), and mention talks on this topic at the 2014 ASM. This advice should also have mentioned the presentation at this same meeting by Dr. Maria Brandl. Her group at the USDA, and others, showed that human pathogens are not terribly happy on the dry and nutrient-limited surfaces of a vegetable leaf, however damage by harvesting equipment, plant pathogens, or senescence can cause plant cells to release their banquet of nutrients, enhancing the growth of non-native bugs such as E. coli and Salmonella. Therefore, another recommendation is to be wary of older produce or that with obvious damage.

Thank you for what you folks do, keep up the outstanding work, and Michele, let me make a prediction for November 21, 2015. Penn State 35, Michigan 27.

Cheers folks,

Edward G. Dudley, Ph.D
Associate Professor of Food Microbiology

1 http://www.foodsafetymagazine.com/magazine-archive1/augustseptember-2014/food-safety-at-farmers-markets-a-reality-check/

2 Scheinberg, J., S. Doores and C.N. Cutter. 2013. A microbiological comparison of poultry products obtained from farmers markets and supermarkets in Pennsylvania. J Food Safety 33:259–264.

3 Scallan, E., Hockstra, R. M., Angulo, F. J., Tauxe, R. V., Widdowson, M. Roy, S. L., Jones, J. L., and P. M. Griffin. 2011. Foodborne illness acquired in the United States – major pathogens. Emerg. Infect. Dis. 17: 7-15.

TWiM 108 Letters

Nervous in San Diego writes:

Dear Professors of TWiM,
I was recently introduced to TWiM by a neighbor. For the last few weeks I have been listening to the backlog of TWiM podcasts, mainly while walking our dog. Regrettably, our dog is a lousy conversationalist. Listening to TWiM while walking is therefore a major improvement. As we walk, the dog investigates things I can not see, while I listen to you talk about them.

Because I have no background in microbiology I must deduce the meaning of the five, six and seven syllable words that you use so effortlessly from the clues provided by the occasional simpler words that surround them. I think it is fair to say that microbiology is the study of what can not be seen using words that can not be pronounced.

The other day our dog and I were listening to a TWiM podcast. (In truth, I was listening and she was otherwise occupied.) You were describing how some parasites modify the behavior of their hosts to the advantage of the parasites. Because I was nearing the end of our walk — and the podcast was not yet complete — I decided to take another lap around the block.

It suddenly occurred to me that TWiM was modifying my behavior. My decision to extend my walk seemed substantively the same as the behavior of a grasshopper afflicted with Summit Disease. As I continued thinking about this phenomenon, I surreptitiously checked my mouth for evidence of frothing, while resisting the urge to climb a telephone pole.

Fearing the worst, my first thought was to rip off my earphones to rid myself of the TWiM infection. But, before taking such a drastic step I decided to solicit your expert advice.

Questions: If listening to TWiM is capable of causing me to walk further, is it possible that you are also inducing behavior changes that I have not yet recognized? Will I soon start craving pickles or become addicted to reality TV? Would it be safer for me to restrict my future podcast listening to Car Talk? I await your response with some trepidation.

Nervous in San Diego
P.S. The weather here seldom changes, but I’ll leave it to my neighbor Elio to provide the details.

Pavlina writes:

Hello, This Week in Microbiology,

First of all, your podcast is amazing, it made my microbiology preparation much easier in university and got me curious about many things.

Now, I've listened to the battle for iron podcast and one thing that I couldn't find on Google got me interested. What is the exact etymology of 'ocelloid'. It was mentioned the word has something with "eye" inside of it and I had to look it up but nothing really came up. Do you by any chance have any idea where it might have come up from?

Thank you in advance,
keep being awesome!

Best wishes from Bulgaria.

Alice writes:

In response to the letter from Mark:

Besides West Nile and other mosquito-borne illnesses, fungal diseases leap to mind. Dry soil becomes dust that can be inhaled. Coccidioidomycosis (aka Valley Fever) is probably most relevant to California. There is an open access systematic review available from Plos Currents that may be of interest.


Alice I. Sato, MD PhD
Assistant Professor
Pediatric Infectious Disease
Albany Medical Center

PLoS Curr. 2013 Jun 5;5. pii: ecurrents.dis.7a2cee9e980f91ad7697b570bcc4b004. doi: 10.1371/currents.dis.7a2cee9e980f91ad7697b570bcc4b004.

[Mark had asked: How do drought conditions change public health risks? CA is now experiencing higher incidence of West Nile virus infections (TWiV listeners will recall Prof Despommier has explained mechanisms coupled to drought and mosquito habitats several times). Should other risks be expected? Or shifting between risks?]

TWiM 107 Letters

Jim writes:

Hi Vince,
For your interest in listening to physics, there is a podcast called The Titanium Physicists Podcast. They use a conversational format similar to what you use. They have a panel of experts and a guest who is not a physicist but who is accomplished in some other area. BTW I recommended the twix group to him when he was looking for a biology podcasts.

Love the 4 podcasts you people do.

Lisa writes:

Hello TWIM overlords,

I have been listening to this podcast since it first came out in 2011. Now I am an incoming senior at UC Berkeley majoring in Microbial Biology. It was your podcast that helped me decide what to study. I would also like to say hi to the graduate student that captured fruit flies with wine; perhaps we have already met.

It's summer for me, and I have been re-listening the podcast. Everything is glorious, but what caught my attention is TWiM #48: It's all about direction with Jo Handelsman. This was released in 2013 and it talked about the deficiency in science educated workers in the bachelors level. I was hoping in working in a startup or in industry for a year or two before I went to grad school for a phD, but should I bother at all? I don't plan on going to academia, and I don't know what to do about further education. My grades are not the best but I'm a student researcher in a lab up in the hill and I enjoy research. I have a lot of autonomy in what I can do and I'm afraid I'll never regain that sense of freedom without a phD -- at the same time, I don't want to get lost in constant paperwork. Berkeley has a lot of academics so I don't know what it's like in industry. I do enjoy it when you guys bring it up in the podcast.

This podcast was the fodder to keep me going through bad semesters. At first, they all seemed fascinating and quite confusing. Now I understand more, but more importantly, I'm questioning the paper and thinking about what the data means. I still have a long way to go, and in a way, I feel like I have learned nothing because there is always so much. I would like to thank all the hosts of TWiM for being part of my high school and college experience. I still have a year left in college but I should have thanked you three years ago when I first got accepted.


Kathy Spindler writes:

In the late 1970s, when there were a couple of years of droughts in California, the complete saying was, "If it's yellow, let it mellow. If it's brown, flush it down." And a very memorable billboard I saw in the Central Valley showed someone in the shower with the caption, "Sing shorter songs."

I enjoyed crossing over to TWiM 104 to hear the measles story covered!


Steve writes:

Hi Vincent et al,

I was just listening to your TWiM 41 interview with the HealthMap man, and called it up, to have a look. There were a couple of red dots, not far from me--one a mystery illness making an EasyJet plane turn back home--and the other, this shocking news about the, endangered, Saiga, antelope. It does not seem that long since I was watching wildlife programmes that featured migrations of, seemingly, limitless numbers of these animals: now we hear that they are being wiped out with extraordinary speed, by what is thought to be a bacterial infection.

It seems to be happening almost impossibly fast. Perhaps the team would like to look into it for your podcast.


All the best,


Weather still rather grey and windy (But I don't get out, as I'm housebound with ME, and can only stay upright for a few minutes at a time.).

[also see Zimmer article: http://www.nytimes.com/2015/06/02/science/saiga-antelope-mystery-disease-die-off.html?_r=0]

Wink writes:

Loved your SNP. In addition to washing produce, only reverse your stomach's HCl when necessary. (Also, the STEC dose is lower than Salmonella.)
Wink Weinberg (Atlanta)

Stuart writes:

Greetings from sunny Seattle! Where its 21 degrees C with clear skies.

Because you asked...Here are my 2 cents on the whole handwashing situation that has been discussed over the past few episodes.

My solution would be to change building codes to require shared sinks for men/women that are located outside the actual bathroom.

This would ensure compliance because it would allow for policing without violating any privacy issues. It could be especially effective in a restaurant setting where a manager could simply discipline employees they watch leave the restroom without making the required stop at the handwashing station located outside.

Additionally, some peer pressure and social stigma would be enough to guilt people into not skipping the handwashing station. Behavior might change if poor hygiene is on display for everyone to see.

Thanks for the great podcasts! I am a fanatic Twiv/Twim fan and listen to the podcast on my 1 hour commute to my job in a manufacturing lab @ a biotech company.

Long time listener, first time email-er.


TWiM 105 Letters

David writes:

Greetings podcast team,

I'm a long-time listener to TWIM and TWIV and if I had a longer commute I would get TWIP in the mix too. Only so many hours in the week!

I am a research tech in Portland Oregon, where our dry mild winter has given way to a gorgeous dry mild spring. Currently 57F and sunny. 2015 to date has been bad for farmers (and skiers) but pleasant otherwise.

I wanted to commend you all for taking on papers and questions outside of your specific areas of expertise, because the conversation that ensues lets us listen in on how you think about science questions.

If you had all the answers at your fingertips it would be highly accurate but of less interest and utility for me at least.

I wanted to weigh in on the mandatory handwashing sign question because I think it is a Trojan horse. Libertarian politicians and letter writers claim they want to see freedom of choice for consumers so free markets can make everyone's lives better but the handwashing argument is a pretty clear tell regarding their true intentions.

Since handwashing is the slightest of inconveniences to the restaurant worker and has no downside for the consumer, it's hard to believe that they are truly driven by their desire to be able to buy a meal at a restaurant where the employees have not washed their hands.

I am convinced until I see some persuasive arguments to the contrary that each time you hear about this free market handwashing topic the real motivation of the person putting this idea out in the culture is to normalize the idea that government in general and regulation in particular is bad, and they really care about their favorite business interest believed to be oppressed by Washington, not oppressed cooks who'd rather have dirty hands.

What I'm really curious is how the independent certification would work. Why are third party monitors watching us wash up better than a government mandated sign? If the government was keeping an eye on us in the bathroom they'd be marching in the streets!


Bob writes:

Hello again - I just listened to the Red Queens discussion about iron battles on TWIM 103. Regarding your interest in other occurrences of this phenomenon there is a paper by Roy Jensen et al at http://www.ncbi.nlm.nih.gov/pubmed/?term=24616884 where he discusses in detail the battle for tryptophan between Chlamydia and their mammalian hosts.


TWiM 104 Letters

Mark writes:

Hello TWiM-aggregate,

Its warm and sunny Spring weather here in California’s Bay Area. The fourth year
of Drought is upon us - please send water.

Speaking of water, below is a humorous incident that could be used to draw
attention to MRSA or proper hand hygiene. These are probably better suited to
informal settings like the bar instead of the classroom, but here goes ...

A town in Texas televised their 4/28 city council meeting. The mayor recognizes
the mayor pro tem who starts to talk about raising MRSA awareness in their
community, sharing personal experiences with MRSA victims.

The mayor leaves, and the mayor pro tem continues to talk. Male urination sounds
can be heard and snickering starts. A loud flush is heard and the mayor pro tem
erupts in laughter, which continues as the mayor returns to the council room. He
obviously didn’t wash his hands.

Within days a video clip “went viral”. My friend sent me the link 5 days later.
When I saw it on YouTube it had 1.3M views. The Houston TV news picked it up -
watch it here: http://cbsloc.al/1JLDdAk

This real life event quoted from the venerable, sophomoric movie “The Naked Gun.”
Detective Frank Drebin (bio: http://bit.ly/1R6Tpyc ) had a similar, highly
fictionalized urinary mishap with an open mic:

Fortunately TWiX shows are produced with tethered microphones.

Speaking of drought: in California 80% of the water supply is used by
agriculture. Our now, maladapted water policies reward growing high water
consuming crops, like almonds or rice, for export . CA Governor Jerry Brown has
declared a water emergency and is seeking to have households reduce usage in the
range of 25-33% compared to 2014.

People who support conservation efforts have a handy phrase “if its not brown
don’t flush it down.” People critical of the governor have morphed this into
“it its Brown then vote it down”.

Let me end with a serious question:

How do drought conditions change public
health risks? CA is now experiencing higher incidence of West Nile virus
infections (TWiV listeners will recall Prof Despommier has explained mechanisms
coupled to drought and mosquito habitats several times). Should other risks be
expected? Or shifting between risks?

All the best.

Suzanne writes:

For anyone interested in trapping fruit flies without drowning them, you can put a little wine (or I use a piece of overripe banana) in a container with a small hole in it. The flies get in but can't usually find their way back out. You can then take them outside and release them. Every now and then when the contents are particularly alcoholic smelling, it seems to me like the fruit flies are slower to fly away... as if they were drunk!

I was glad to hear someone write in in favor of your using the word Talmudic for your questions. It's really the perfect word for unanswerable questions that are worth asking just for the thinking. This atheist also approves. Talmudic questions and midrash are traditions more people should know about just because having a questioning culture is an important and useful thing, I think.

Thanks for all you all do.

John writes:

I have a few observations and comments about the TWiM 101 and 102
letters about hand washing rules.

1. In his book _Fast Food Nation_ Eric Schlosser discusses the
relative abilities of regulators and consumers to change food safety
practices. Consumers were a powerful force cleaning up
slaughterhouses because there was a media frenzy after the Jack in the
Box outbreak.


2. The bathroom sinks where I work dispense a trickle of cold water.
If you let them run for 5 minutes you get a trickle of warm water.
Pathogenic bacteria are laughing all the way to the kitchen. "Green"
building rules may make the hand-washing debate irrelevant.

3. In my experience doctors and dentists wear gloves but do not wash
their hands in my presence. Freakonomics covered the difficulty of
getting doctors to wash their hands:


4. The traffic law analogy on TWiM 101 leads to the opposite
conclusion than the one proposed.

You can build a road network without signs and signals. In Europe the
term "naked streets" is used for unregulated urban areas. They work
as well as hyper-regulated American streets.

We keep forests of signs around for comfort, because people
erroneously think "it can't hurt." It can hurt. There are books of
guidelines for predicting whether road signs help or hurt. Traffic
engineers don't follow the books because the boss already "knows" more
regulation is better. When you start "this week in transportation
policy" I'll write a few thousand more words for you.

Lawyers use terms like "penumbral crime" and "aspirational law."
These are laws that aren't expected to be obeyed, aren't taken
seriously, and teach us that we have to decide for ourselves which
laws to obey. Everybody who drives breaks the law, and I include
those who say and even believe they don't.

Inspectors can enforce laws requiring signs saying "hands must be
washed." They can not enforce laws saying hands must be washed.
Given that we have a finite number of inspectors, what do you want
them spending their time doing?


TWiM 103 Letters

Bailey writes:

Hey Vincent, Elio, Michele and Michael!

I'm a first year microbiology graduate student at UC Berkeley and an avid listener of twim. Elio's snippet from the most recent podcast reminded me of a personal anecdote that might be useful to share with listeners. The snippet was about the volatile compounds produced by yeast that attract fruit flies and cause dispersal of the yeast. A couple months back I had a small problem with fruit flies in my apartment and decided to try the home remedy of apple cider vinegar and soap to get rid of the flies. The apple cider vinegar is supposed to attract the flies while the soap breaks the surface tension causing the flies to become stuck and eventually drown. This concoction helped get rid of some of the fruit flies, but there were still a few buzzing around after a couple days. That weekend my roommates and I drank a bottle of wine to help de-stress from the hardships of graduate school. We left the bottle out on the counter with only a couple centimeters of wine left in the bottom and the next morning it was filled with fruit files! It seemed that the volatile compounds in the wine were much better at attracting fruit flies than the compounds in the apple cider vinegar.

It was very interesting to hear about the molecular basis for this aroma-based communication between yeast and fruit flies. For any listeners who have come back from spring break or a weekend away and now have to deal with fruit flies I would recommend using this wine trap! It seems a little bit evil to be luring fruit flies to their death with the scent of a presumed feast, but it works beautifully!

Anyways, keep up the good work guys! :)


John writes:

Dear TWiMmers,

I can't believe I'm writing in about this, but I have to say that I was rather deeply offended at listener Dave's insistence on policing your use of the word "Talmudic" on TWiM.

I am a religious Jewish scientist. Part of my experience is the understanding that my colleagues, who often discuss their Christianity, Atheism, Buddhism, Islam, Sikhism, Taoism, Shintoism, and other religious -isms, are as tolerant and respectful of my Judaism as I am of their beliefs.

Science is a human endeavor, and scientists have beliefs and cultures. These do not affect the judgment of a professional scientist, but having diverse cultural perspectives and an uncensored environment is an asset to scientific pursuits.

Silencing religious, or even formerly religious, scientists stifles the pursuit of science. Science should take all comers provided they pursue unbiased interpretation of data. There is nothing about the word "Talmudic" which implies you'd pursue anything else.

The Talmud is an ancient Jewish cultural artifact. It preserved many of the basic logical techniques of the Hellenistic world, and was a building block of the intellectual tradition that gave birth to modern science. My own studies of the Talmud taught me to value the importance of free inquiry and discussion that relies on evidence and logic.

There are enough places where Jews face harsh consequences for speaking the words of our culture or sharing our intellectual traditions. I have gravitated to science in part because I feel safe among intellectuals who respect the value of my ancient culture.

I enjoy TWiM partly for its "Talmudic" questions, which remind me of the long, unresolvable arguments that I learned as a child. It's a quintessential rehearsal of science: the exploration of questions that we know we will never answer to our satisfaction, but that are explored because of the invaluable lessons that will be revealed for the asking.

It makes me smile and feel welcomed every time I hear Dr. Schaechter say "Talmudic Question." I would hate to see a fun and enjoyable exercise be marred by the views of a listener who cannot tolerate a single word from a culture that differs from his own. I would never have complained about an "Atheist Question" or a "Madrassa Question." I am appalled that Dave would think it appropriate to scold you and attempt to police speaking in a way that is informed by your participants' culture.

Thanks for all the work you do, and I am sorry if anything I've said is impertinent. I just couldn't believe what I was hearing when you read Dave's letter.



Dennis writes:

Dr. Vincent and the Twixers,

At some point this sudden wave of deaths in a small southeastern Nigerian town might become a potential twix topic (see link below) unless it turns out to be poisoned food or water. Separately but instigated by this, a thought-question occurred: as unlikely as it may sound, are there other vectors besides viruses, microbes, parasites and poisons from known toxins that could be "contagious" and which could kill quickly? For example could somebody use CRISPR-CAS9 to modify a common benign bacterium to deliver a toxin? Ugh.

Fanboy of TWIX,



Anthony writes:

Contagion MAP -- A brief history of malaria, leprosy, and smallpox.

I don't know if this is accurate or if it's been featured already, but
perhaps it might be of some interest for TWIM.

And this is a few years old and again I don't know if it's already been covered.



Thank you,



TWiM 102 Letters

Dave writes:

TWIM Comrades--
I first want to compliment you on one of my most listened to podcasts, and one that I actually know what is being presented most of the time.

Now about the term Talmudic.
Do we need a name that is a legal commentary on the Torah, explaining how its commandments are to be carried out., all 613 of them, on a science podcast?

Religion is so prevalent in everything in society, from media, politics, holidays, and visual statements that are overwhelming.

The liberal view of the "belief in the belief in religion" is not questioned (as Dennett has explored).

But please, don't let it creep into the sanctuary of sanity and reason that is TWIM.

Suzanne writes:

In my experience working in food service, you're all right. There's no good way to mandate and police handwashing. But that's not really the way it works, anyway. The education is mandated and best practice rules are set and when the regulatory agencies check up on you, they take points off for each thing that doesn't measure up. And it's true that the rules aren't followed perfectly, but if you aren't doing well enough you get corrected or closed down before your customers even notice most of the time. Without the rules, believe me, a lot of people would go with the "well I don't do this at home and it's never hurt me" philosophy and things would be even dirtier than they are. It's true that when enough people got sick you'd lose customers. It's true that in the end the free market would probably take care of each individual case. But the free market is a lot slower than regulation and tends to require more hurt and death to create change. It's also true that without regulation private groups often jump in to fill the void. But we often have less influence when we try to make change with money rather than votes and due diligence is often difficult at the individual level. Everything requires more participation than US citizens are interested in these days to keep things running smoothly and well. It's just as easy to relinquish your personal responsibility to the "free hand of the market" as to the idea of government as something there to take care of you instead of something we all are supposed to be a part of.

P.S. The health departments that are in charge of enforcing the code are not staffed by the restaurant industry. Other enforcement agencies don't need to be staffed by members of industry, either. Scientists and people from a more academic side of the fields would know just as much as business owners and employees. It's just been policy for a while now to allow the revolving door between industry and government jobs.


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