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mailboxTWiM regularly receives listener email with corrections, comments, suggestions for show topics, requests for clarification, and additional information. A selection of these is archived on this page.

TWiM 76 Letters

Geoffrey writes:


I just got around to listening to episode 12 “Photothermal Nanoblades and Genome Engineering”. Your comment that it would need to be scaled up before it was practical for some of you to use intrigued me. I did a quick Google search and I didn’t see any recent articles addressing scaling up the process though I’m sure that there are groups working on it. In my own amateur fashion, I’d like to suggest an approach to such a process.

I believe that technology applying microfluidic flow cells to single cell streaming is reasonably well-developed currently and improving all the time. If you installed the insertion capillary tube into a microfluidic flow cell and added a photo-sensitive trigger to the capillary tube, then it should be fairly practical to mass insert bubbles of materials into cells fed through the flow cell and collected on the other side. Although flow cells would, most likely be tailored to particular cell sizes, it might be possible to make the insertion point slightly generic (i.e., slightly larger) by using laser forceps to automatically direct and immobilize the cells during insertion.

The main restriction would likely be finding a cell culture that would support the microbe in question with sufficiently low viscosity so as to flow through the cell with ease while prevented undesirable cellular effects (such as clumping or lysing) while the cells are waiting to inject. High cell density at the input reservoir could probably be achieved by centrifuging the initial culture then micro-diluting up the resulting pellet.

Although this may not prove to be the most efficient way to mass-process cells, I do see another potential advantage in using a microflow cell. With additional solvent input channels before and after the insertion point it might be possible to chemically manipulate the cell’s immediate environment for periods of milliseconds to seconds in such a way as to make them momentarily more amenable to insertion without long-term consequences to cell survival. Such manipulations would be easy to study, cell species by species in these flow cells until a manual of cells and optimum manipulation conditions could be generated.

Anyway, thanks again for the fascinating look at research that I don’t get a chance to look at very closely often (or understand).


Tarwin writes:

25c in Palo Alto, California.

I think humans (us) are so enthralled by the idea and stories of symbiosis because we see it as unusual. Even though our world is full of symbionts, life relies on symbiosis, we are blind to it most of the time until extraordinary examples are pointed out to us. These make great examples of the "precision", depth and complexity of evolution and of life.

It's easiest to make a headline in our mind when we see "small" examples of tightly woven systems than to keep the whole ecosystem of metabolism in our minds.

Thanks as always for the amazing education and entrainment,

Tarwin - Developer / Designer

Jacob writes:

Hi all,
Just wanted to make a point about organelles vs symbionts.
You suggested that the difference might be that if all cells in the organism have it then it is an organelle; however not all plant cells have chloroplasts.
Might the difference be just how high up the taxonomic tree the symbiosis goes?
Sydney, Australia.

Marion writes:

TWIM 74, about 26 minutes in.
the difference between enbosymbionts and organelles is:
1. WHEN it happened and
2. how much it increased fitness.

the endosymbioses that resulted in mitochondria and chloroplasts happened many billion years ago and apparently conferred selective advantage to recipients cells (future eukaryotes) over nonrecipients (future prokaryotes). we only have to wait a few billion years to see if the same is true for the endosymbionts discussed.

Bernadeta writes:

Dear Twim team,
Thank you for all the great episodes; I'm loving every single one of them!

I'm very pleased to hear more discussions on fungi-related subjects, being from Lithuania myself, I wait every year for the mushroom season, so that I could go and collect them. We even have national competitions for who can collect the largest number of mushrooms or find the biggest variety of them :)

On the mushroomy note, I would like to draw your attention on a recent paper describing the first fully sequenced genome of arbuscular mycorrhizal fungus, I think it's worth discussing.
"Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis" .

The second paper that caught my eye, was describes how S. aureus "intentionally" induces pain through neurone stimulation, in order to suppress immune system's response to the infection. I think it very much makes one think about systemic control of the immune system and, as ever, the unexpected ways that bacteria have evolved to evade it.

"Bacteria activate sensory neurons that modulate pain and inflammation"

Best wishes,


TWiM 75 Letters


Timothy writes:

Hello TWiMsters! I recently discovered the trifecta that is the TWi series, and now I can’t get enough of your discussions of all things micro. For graduate students like myself, keeping up with the scientific literature can all too easily become just a means for cramming information into our brains that we feel we “should” know. Not only do your shows keep my mind stimulated and expose me to scientific papers that I might not otherwise read, but the informal and enthusiastic nature of the programs are just the slap in the face I need to crawl out from under the stack of papers, and remind me that I actually love to learn about science and to think about the various implications that a particular finding or result might have. After listening to your conversational discussion format and your fantastic insights that tie together the biology of the organism (or virus – are viruses organisms?) with the environment, host, experimental techniques etc., I am finding new clarity in the way that I think about scientific problems and evaluate scientific papers. I can’t commend you enough for what you do. Formal presentations of scientific findings are a dime a dozen - listening to world-class scientists “chat” amongst themselves about current topics in microbiology is an invaluable resource that few people really ever get a chance to do, until now. THANK YOU!

On a scientific note, I was recently listening to TWIM #43 and your discussion on the stable formation of caveolae in in E. coli. It was mentioned that it had previously been thought that stable caveolae formation in eukaryotic cells requires cholesterol, to which Michael replied that “there is [no cholesterol] in our friends the bacteria”. Although this was and is true in the context of E. coli and the paper’s findings, I think it is worth pointing out that there are several described examples of free cholesterol and cholesterol-containing glycolipids in bacterial outer membranes – namely in Helicobacter, Mycoplasma, Ehrlichia, Anaplasma, Brachyspira, and Borrelia species. In Borrelia burgdorferi, cholesterol containing compounds have been shown to form organized lipid rafts both in culture and in animal-derived organisms, with physical properties similar to that in eukaryotic membranes. A recent paper published in PLOS Pathogens in January of 2013 utilized fluorescent and radiolabeled cholesterol to demonstrate that B. burgdorferi extracts cholesterol from the plasma membrane of eukaryotic cells, and that prokaryotic cholesterol-glycolipids can be transferred to epithelial cell membranes through both a contact dependent mechanism (using direct attachment) and a contact independent method (through released outer membrane vesicles). I highly recommend looking in to this story (maybe as a TWIM topic?), as it provides a shift in the thinking about lipid rafts, expanding their biological relevance to prokaryotes, and could have implications for the evolution of the eukaryotic cell membrane structure. Additionally, transfer of antigenic lipids from bacteria to host cells could play a role in pathogenesis - having multiple consequences for the host immune response and potentially contributing to heightened inflammation, and perhaps even direct targeting of the cells themselves by immune effectors. I’ve provided the citations and Pubmed links to a few papers on the B. burgdorferi story below, but also recommend digging into the story for H. pylori.

I’ve rambled enough for now, I should run – I’ve got to get to iTunes to write a good review or two…

LaRocca TJ, Crowley JT, Cusack BJ, Pathak P, Benach J, et al. (2010) Cholesterol lipids of Borrelia burgdorferi form lipid rafts and are required for the bactericidal activity of a complement-independent antibody. Cell Host Microbe 8: 331–342.

Crowley JT, Toledo AM, LaRocca TJ, Coleman JL, London E, et al. (2013) Lipid Exchange between Borrelia burgdorferi and Host Cells. PLoS Pathog 9(1): e1003109.


Timothy Casselli
PhD Candidate
Department of Veterinary Microbiology and Pathology
Washington State University

“The truth is incontrovertible. Malice may attack it, ignorance may deride it, but in the end, there it is.”
- Winston Churchill

Alicia writes:


During TWiM#46 it was discussed that spores are able to sense peptidoglycan that has been shed by other bacteria. I would like to know, are the spores able to differentiate between the peptidoglycan that is shed by growing bacterial neighbours and the peptidoglycan lost during lysis.

Thank you,

Alicia Zigay
University of Victoria, BC, Canada

Jon Dworkin answers:

Excellent question! If this any indication, your listeners are really paying attention!

Spores are able to differentiate between peptidoglycan fragments generated from growth and those generated by lysis since these processes in fact produce different PG fragments. Those resulting from lysis are thought to be produced largely by lytic transglycosylases which generate PG fragments containing an anhydro (non-reducing) end, whereas fragments produced in growth do not contain this group. In collaboration with Shariar Mobashey, an excellent PG chemist at Notre Dame, we demonstrated that synthetic muropeptides containing an anhydro group do not stimulate growth but synthetic muropeptides that lack this group are able to stimulate spore germination. Thus, spores can differentiate between cells in the milieu that are lysing versus those that are growing.

Bill writes:

Finally, I can send an intelligent comment (re: TWiM #51) ...


bill mackintosh

Frank writes:

Dear esteemed doctors,

I am sincere in this appellation as one of your many listeners who depend upon your unbiased fact finding and enlightening delivery to both educate and debunk with the latest information.

You have often remarked on the contradiction of the numerous pathogenic bacteria in common public areas while you as individuals do not feel endangered. In commenting on a letter read on TWIM 72 you mentioned the "cloud" of toilet-originating microbes created with every flush, yet a lack of evidence of resulting disease. It comes up also in regular mentions of door knobs, railings, phones and other public conveniences. Often this is attributed to the protection provided by a healthy immune system.

My question is whether the mechanism of microbial balance achieved in the human microbiome should be applied to understanding the forces at work in these external environments. Might our Linus-like microbial cloud function like the often mischaracterized schmutzdecke which purifies much of our drinking water?

Analyzing the potential health affects of environmental microbes apart from the greater human and environmental microbiomes seems a bit like analyzing the path of stars orbiting the earth. Am I wrong to assume that the microbial community of the toilet, room air, hands, nose and mouth have a significant impact on the danger from most of the individual microbes within those communities?

It's 252 degrees absolute, (or minus cold aught six on the Retrograde scale) this morning in sunny Connecticut.

A sincere thanks to you all for your dedication to TWIX. The world is listening to you more intently every day, and better for it.

Best Regards,



TWiM 74 Letters

Katja writes:

Thank you for the great podcast! You've explained our story very well and it was funny to listen to it. I didn't know that "Speak friend and enter" is from lord of the rings! I just wanted to explain the name CYCLOPS because this was a question mark in the podcast. This is a link to Yano et al. 2008 where they describe the cyclops mutant phenotype in fig. 1. In the WT the fluorescently labeled rhizobia enter the root by the formation of an infection thread. In the cyclops mutant, the root hair curls around the bacteria but further infection is impaired. And because this looks like an eye of an cyclops, the mutant derived its name from :-)

Laurel writes:

Hello all! I am a graduate student at UNC Chapel Hill in the Microbiology & Immunolgy department, and since my lab is mainly focused on the immunology section of that I try to supplement my microbial knowledge with information gleaned from other sources like your podcasts (Though I am a particular fan of parasites and TWiP). And as you can probably tell from this comment being so behind, I am never caught up with the podcasts, though I listen to them regardless.

You all mentioned that perhaps due to the high salt levels and temperature of the lake the haloarchaea from TWiM 68 act very similarly to when you perform a transformation in their extremely high gene transfer rate. Wouldn't it be fairly easy to test this theory since the authors demonstrated that they grow at many different temperatures? You could follow growth at room temperature and examine if comparable gene transfer takes place. I just wondered if any had considered looking into that to determine if that is the case. Thanks!


Geoffrey writes:


While your show has been a real eye-opener for me in so many ways, much of my interest in the microbial world remains in the areas of endo- and ectophytic microbes, soil microbial ecology, and food / energy / raw materials fermentation. You speak frequently (and, I have noticed, rather lovingly) of exploratory deep genome sequencing just to try to find out what’s in the environment. Though a little more narrowly focused, that is exactly the kind of research that I am reading about frequently in my areas of interest. What is the microbiome of a Withania leaf?, miso?, apong (wine / beer from moldy rice)?, hydrogen-bubbling mud?, and other topics of that nature.

I won’t pretend to understand all the techniques that are being used to genetically identify the microbes in these environments but it is of interest to note that much of what we thought we knew due to culture techniques isn’t particularly accurate. Culture techniques often skew results towards easily culturable microbes which can greatly distort our reconstruction of microbial communities (especially reconstructions of microbial succession) and completely misses the contributions of NCO’s (Non-Culturable Organisms). Recent techniques involving direct analysis of DNA present has greatly expanded out knowledge of these communities but different techniques often produce different results. We are still expanding and improving these techniques and, more importantly, learning how to apply them so that they complement each other’s strength and weaknesses and give us unprecedentedly clear views of microbial communities.

With all that introduction done, I now present my question. I assume that deep genomic diving involves many of the same techniques used in the shallower explorations mentioned above and viruses definitely provide a deep and wide pool of NCO’s. Would you be able to discuss some of the major DNA / RNA detection techniques used in this field in terms of their strengths and weaknesses and how different researchers are overlapping their use to build robustness into their studies of microbiome and virome?

Thanks for the great podcast,


Alice writes:

First, thanks to Vincent et al for the wonderful podcast series (all 3). I am a fellow in pediatric infectious diseases (a fellow is the MD-equivalent of a post-doc for subspecialty training). Your podcasts are thought provoking and timely and always intellectually stimulating - so thank you.

In return, the temperature here in Cleveland Heights is currently 15oF, winds west at 7mph, humidity 72% and I'm really tired of winter.

Regarding TWiM #72: your discussion of this paper coincided with my caring for a patient with a surgical procedure known as a ureterosigmoidostomy, in which the ureters are implanted into the distal colon when the bladder is not present or can't be used for some reason (e.g. congenital malformation). In the process of caring for this person, I learned that there is a significantly increased risk of cancer developing in the bowel (see references below). After this surgery, the urine drains into the bowel and greatly changes the chemistry and flora present. Examination of the microbiota and/or metabolome of these patients may turn out to be quite interesting.

Thanks for making me think differently about our relationship to micro-organisms every day.

Alice Sato, MD PhD

1. Eur Urol. 2011 Nov;60(5):1081-6. doi: 10.1016/j.eururo.2011.07.006. Epub 2011 Jul

Tumor growth in urinary diversion: a multicenter analysis.

Kälble T, Hofmann I, Riedmiller H, Vergho D.

2. BJU Int. 2010 Mar;105(6):860-3. doi: 10.1111/j.1464-410X.2009.08811.x. Epub 2009
Aug 13.

Long-term outcome of ureterosigmoidostomy: an analysis of patients with >10 years
of follow-up.

Tollefson MK, Elliott DS, Zincke H, Frank I.

3. Acta Chir Belg. 2009 Jul-Aug;109(4):531-3.

Complications associated with ureterosigmoidostomy--colon carcinoma and ascendens
infection resulting in nephrectomy: a case report.

Turedi S, Incealtin O, Hos G.

4. J Urol. 1990 Sep;144(3):607-10.

Current status of tumor of the bowel following ureterosigmoidostomy: a review.

Husmann DA, Spence HM.

Clark writes:

I was wondering if you all had seen this recent paper on detection of oral bacterial DNA in synovial fluid. Given that one of the frequent hosts teaches dentists I would be especially interested in his comments about the relationship of periodontal bacteria in other diseases. I think it’d make a very interesting discussion for non-microbiologists like myself. (My background is physics)

A doctor friend of mine created an rss feed on the topic so it seems like there’s been a lot of work done on this.



TWiM 73 Letters

Mark writes:

Hello Team TWiM,

I’ve followed with interest your coverage of Michael’s research into use of copper to fight hospital infection. Of all the interesting papers covered in 2013, I think the one most actionable is episode 55, The Copper Room. His research, described in that and prior shows, addresses an under-reported aspect of our health care system. Hospital acquired infections are a serious matter of which I am especially mindful as I prepare for surgery later this month. Kudos to Professor Michael Schmidt for proving how a relatively simple change of hospital materials can have a huge impact on improving patient health and outcomes.

Let me share some news, and ask follow-up questions.

Monday, 1/6/14, at the Consumer Electronics Show, Corning Inc introduced a new line of “Gorilla Glass” that it claims is the "World’s First Antimicrobial Cover Glass”. Links with information:

— press release:

— video releases:

Corning is positioning the product for touch-based mobile devices to combat bacteriological growth and spread of disease. We have all have seen phones whose surfaces are, in plain speech, gross, disgusting and covered with layers of schmutz. TWiM listeners would call such objects “fomites” to use a polite, abstracted, and neutral term.

Here come my questions ….

1. Corning highlights the use of “ionic silver” as the antimicrobial agent in its new glass. Silver, Ag, is in the same column and one row below copper, Cu, in the Periodic Table. Below silver is gold, Au. Do I recall my chemistry correctly in that each has the same number of valence electrons? If this is true, can Michael or other hosts compare-and-contrast how Cu/Ag/Au vary in effectivity killing bacteria? Besides economics, is any of those metals a preferred choice for bacterial killing agent? Why, or why not? Is the preference related to their increasing conductiveness as you descend rows in the Periodic Table?

This question is truly cutting edge… I call your attention to

2. Would you describe in more detail the mechanism by which copper’s valence electrons kills bacteria?

3. What impact does copper have on neutralizing viruses and their ability to spread? I use “neutralizing” because you can’t kill a non-living virus. Do you agree with this phrasing?

Wishing all of you the best in 2014.


PS - the weather. Here in the San Francisco Bay Area the weather these past few days was mostly sunny, with highs in the mid-60’s and lows in the mid-40’s. This east coast refugee empathizes with easterners like TWiM’s Michiganders, Carolinians, Jerseyites, or his brother out on Long Island who have been experiencing extreme cold with daily highs in the low-teens. Only Elio’s San Diego has better weather as I write this.

CN writes:

Greetings Vincent and Team,

On the foremost, thank you for your excellent educast. Your podcasts has helped me generate and understand a lot of ideas which i would have never accomplished had it not been for your podcast. I have just joined, Dept of Neuro-Microbiology, NIMHANS, Bangalore, India as a PhD scholar. Maybe i can consider it a TWiX bump.

The issue of Health Care associated infection has come up, multiple times in your podcast. I have a query in connection with the same.

Hospital environment harbors microbes usually of MDR type. The ones commonly involved in Nosocomial infections are often environment and antibiotic resistant types. There is a very limited scope of competition from harmless and less robust environmental flora. I'm curious if we could (theoretically at least) introduce environmental flora into hospital regularly, which would then reduce hospital acquired infections. Just a wandering thought.

I always have wondered why doesn’t TWiM have Pick of the week. Keep up your excellent work. Never ever stop TWiX.

A yet another TWiX Podcast fan.

Mark writes:

Hi Vincent, Elio, Michael and friends,

Firstly, thanks for the show. It regularly blows my mind, and keeps me very engaged during the otherwise cold and rainy walks into work. Keeping up with each episode has very much broadened my mind to microbiological topics that I wouldn’t have come across otherwise, which has in turn enriched my own thinking and work.

In the fascinating TWiM 68 ‘The Fungus Among Us,’ Elio questioned the existence of uninhabited aqueous environments. I know of two naturally occurring habitats on the earth that are most probably functionally sterile (that is, supporting no active growth). These are Discovery Basin in the deep Mediterranean and Don Juan Pond in the McMurdo Dry Valleys, Antarctica. Both of these are extremely concentrated brines, where the main salt is not NaCl, but MgCl2 (in the case of Discovery Basin) and CaCl2 (in Don Juan). Previous studies report DNA sequences from Discovery basin, but the current thought is that these originate from organisms that live above the seawater/brine interface and have simply sunk into it. mRNA has not been successfully recovered, suggesting that there is no active life. Exactly what property of the brine precludes life is not fully understood; it could be either the dramatically low water activity (availability of free water) or the chaotropic, disruptive effect MgCl2 has on biological macromolecules. Check out this paper which discusses support for a chaotropic barrier to life:

Don Juan is a particularly fascinating place, as it never freezes over despite experiencing temperatures down to -40oC. There is much less published biological data on this environment (none with molecular tools), but it is more chaotropic and more concentrated than Discovery brine, and most microbiologists who work with Dry Valleys lakes consider it a sterile environment. These environments are particularly interesting because of the current paradigm (in astrobiology) of liquid water being the holy grail for habitability, and yet even on the earth there are (albeit rare) examples of aqueous environments that may fundamentally preclude life.

On a different note, I thought you might all enjoy this paper exploring some of the novelties of haloarchaeal genome replication:

I was reminded of it by your discussion of horizontal gene transfer in the archaea. It’s a really nice study and highlights how different and interesting these organisms are when compared to bacteria or eukaryotes. The authors hint toward some profound evolutionary implications in the discussion.

Apologies for the ramblings, and thanks again for all the inspiring discussions.

Best wishes,


Mark Fox-Powell
UK Centre for Astrobiology
School of Physics and Astronomy
The University of Edinburgh

Bradley writes:

If you can find the backstory to this, it would be an interesting TWiM:

"Passenger with possible TB infection pulled from plane"


Nathen writes:

Hello TWIM-ers,
A friend of mine just posted this question on tumblr and I thought you all would be the perfect people to address it:

Question of the day: A strain of Flavobacterium (KI72) evolved the capacity to digest nylon, obviously in recent history. Fine and well. How long will it be until one of the cariogenic bacteria species evolves the ability to digest dental resin? After all, we are putting a lot of it on their dinner table.

Original Article:

Darcie writes:

Hi, great podcast. I just wanted to let you all know that stool taking "the shape of the container" isn't a British-ism. I work in the Micro department of a hospital/reference lab and we use this criteria on a daily basis when testing for C Diff. Specimens that are too formed must be rejected for testing, and we've had many discussions about what makes a stool formed or not; the criteria "takes the shape of the container" has turned out to be the best way to decide if we will reject a specimen or not.

Jesper writes:

Dear Magiis of the Microbes,

In the news here in Sweden there are unfortunately many reports about the spread of C Difficile, and we've had a few deaths as well. Remembering Michaels research about copper surfacing as a means to reduce harmful microbes in hospital settings, it may be of interest to learn that a study has been conducted here to show that using Chlorine and a detailed cleaning protocol reduced infections by 50%. I have not found the publication, but here is (in Swedish) the protocol recommended: Essentially they swipe all surfaces with Chlorine.

Here is another article about the research in a Swedish medical Journal:

I do not want to make the impression it was unknown that chlorine is effective as an antibacterial. CDC knew this (

Thank you all for a very interesting pod cast!

Software Engineer



TWiM 72 Letters

Jim writes:


My name is Jim from Vancouver. I have no formal education in phraseology but am an enthusiastic follower of TWIP, TWIM & TWIV.

Recently I followed a program about yeast infections and the threat to public health they can pose.

My question is would it be possible to isolate the infectious yeast agents and brew a beer that would act as a vaccine against these infections. I understand that the brewing process kills the yeast so there would be no chance of contamination by the dead yeast which would be filtered out in any case. There were plans at one point to add vitamins to beer at one time to improve public health so the idea is not that unusual.

The question is Would this brew provide a heads up to the immune system that would prevent yeast infections from taking hold?

Also, would it be possible to have a TWIF - This Week in Fungus podcast as part of your audio library? There are so many other valid topics that fungus tends to be neglected.

Vince and Dickson, keep up the good work.

Best wishes,


Dallas writes:

Dear TWIMers

I was catching up on the podcasts and in TWIM 64 you discussed antibiotic resistance and connections between animals husbandry use and human disease issues. A recent article in Science “Distinguishable Epidemics of Multidrug-Resistant Salmonella Typhimurium DT104 in Different Hosts” < > seems to indicate a lack of transmission from animal to human populations.

A comment was then made that the same potential transmission problems would be true for aquaculture animals, where antibiotic resistance is also an issue. However, we need to keep in mind that there are very few pathogens for fish that are zoonotic (excluding helminthes that go between bears and wild salmon and seals and some fish) and most aquatic pathogens don’t grow at human body temperatures. Even more important, antibiotics almost triple the cost of fish feed and very few antibiotics are allowed and those are only for a few species. Unlike pigs and chickens, where adding antibiotics to the feed improves the growth rate and decreases feed consumption, adding antibiotic to fish feeds provides no growth effect and actually decreases the animals immune system (Rijkers, Teunissen et al. 1980) – not good for husbandry.

I had previously sent to TWIV the following graph showing that decrease in antibiotic use in Norway salmon production as vaccination solved the problems.

Notes: Use of antibiotics (yellow line) and amount of fish produced (blue columns). The numbers on the leftside are the tonnes of fish; the numbers on the right side are the tonnes of antibiotics.
Sources: NMD & Directorate for fisheries, as cited in Ministry of Fisheries (2002).

Activist organizations, including PEW, have had a multi million dollar “de-marketing” campaign against aquaculture in the US and have succeeded in framing the images in the society.

Other aquaculture myths that are sold to the public by environmental activists are caused by the mandated “color added” label on farmed salmon when you include astaxanthin in the diet, despite the fact that the chemical is identical to the astaxanthin that makes wild salmon pink. In addition, most people in the US believe that salmon and other carnivorous fish require fish meal in their diets and are thus depleting the ocean resources. We know enough about fish nutrition to create totally “vegan” diets for carnivorous marine fish which out-perform fish meal based control diets. However, the ingredients used in these vegan diets are also useful in chicken, and pig diets and fish meal is less desirable for these species (it makes chicken taste like fish and egg yokes grey). Economics pushes fish meal into fish diets, not biology and this whole fish meal issue is manufactured by activists for emotional appeal. If all aquaculture went away, the fish meal market would shift back to pigs, cows, chickens, dogs and cat feeds, just it was before aquaculture was a significant business. The international harvesting of fish meal has been constant for about 4 decades while aquaculture has grown by a factor of about 100 times.

One of my interest in listening to TWIV, TWIM, etc. is related to the observation that aquaculture systems are really controlled by the microbiological ecologies. It is like the complexity of the human gut interactions extended to all inside and outside surfaces. This makes discussions on TWIV about phages sticking their heads in mucus very fascinating to me. This effectively put the phage between its bacterial host and the host’s dinner on the animals surface. A very good location for an ambush hunter phage that has almost no mobility (Brownian motion).

I could go on about how aquaculture can solve the food (meat) problem for the coming 3 billion more people on this planet (better meat yield, better food conversion efficiency, when the animals doesn’t have to stand up or keep warm). The world wide growth rate of aquaculture (doubling in about 8 years) will mean that the talents of the TWIV, TWIM scientists will be required to understand how these microbiological ecologies really work and how to control the outcomes. We are seeing research dramatically increasing in every area relevant to trying to understand and control the microbiological ecologies of these complex systems ranging from probiotics, prebiotics, to specific phages for specific bacterial problems (aquatic phage therapy), but the sources of this research are primarily outside the US. As aquaculture takes over the meat production business with its higher conversion efficiencies, the need for scientists who understand these complex systems will increase. Many of the TWIM TWIV followers will have a bright future opportunity outside of conventional academic research.

Sorry about being a bit long winded. Love your programs.


Dallas E. Weaver, Ph.D.

Robin writes:

Acellular pertussis vaccine

Thanks for the amazing stuff. Shows how much we have yet to learn.

Cough is an endobronchial symptom. Even whooping cough can be temporarily ameliorated by anaesthetising the epithelium by the inhalation of nebulised lidocaine, the technique used prior to bronchoscopy.

My medical school microbiology is almost from the era of hunter-gatherers with their sticks and stones circa 1968.

If the volume of human knowledge is a sphere, the area of our ignorance (the "known unknowns" - h/t Donald Rumsfeld) is the surface of the sphere. The volume increases by the cube of the radius while the area increases by its square. It leads to the correct perception that our area of ignorance is decreasing relative to the volume of our knowledge. However what lies beyond the surface of the sphere (the "unknown unknowns") is beyond our ken: just as Flatlanders cannot grok what's beyond the dimensions of their world, we cannot grok those unknown unknowns.

"Expelling fomites" - Dr. Michael Schmidt

Fomites are objects (usually solid) in the environment which may (usually passively) harbour microorganisms.

Robert writes:

The germ enlarger. Breakthrough in microbiology, which I am surprised is not used today or discussed on TWIM.







TWiM 71 Letters

Zachary writes:

How long does it take to become a microbiologist?

Tim writes:

I'd never heard of magnetotactic bacteria before and thought perhaps you guys might find this interesting. Not sure if you've mentioned these on TWIM before, if so ignore this email.
Microbiology and Molecular Biology Reviews : MMBR 2013 Sep; 77 (3) : 497-526.
Ecology, diversity, and evolution of magnetotactic bacteria.
Christopher T Lefèvre, Dennis A Bazylinski
PMID: 24006473
Tim Zweber
Zweber Farms

Benjamin writes:

I listened to your podcast that discussed the primary literature article "A Burkholderia pseudomallei Toxin Inhibits Helicase Activity of Translation Factor eIF4A" that was published in Science. This article mentions that after the crystal structure for BPSL1549 was determined and they saw that it was a similar structure to CNF1-C, they created a mutated version that was not toxic, which they expected since the same happens in the mutated E. coli version of the protein.

Does this mean that if they find an agent to inhibit the protein that it would likely be able to work on both E. coli and B. pseudomallei toxins since they are similar? And is this a normal technique for treating bacterial infections since by targeting a protein rather than the bacterium it would leave the bacterium alive to make more of the protein toxin?

Thank you,


Ludwig writes:

Hello TWiM team,

Recently I saw an NPR article on a the disease SCID-X1, an X-chromosome linked immunodeficiency disorder where the body has no functioning immune system. I was wondering if I could hear your thoughts on how the microbiota would respond to this. I know prior research has shown that the immune system plays a role in shaping the community composition of the gut flora. How would the microbiota react to a complete absence of an immune system from birth?

Thank you and keep up the great work.

Will writes:

Hello TWiM team,
I’m a senior biology major who is bent on pursuing a career in microbial ecology. Last summer I discovered your podcast and I wish I had started listening earlier. You guys have been so great that you inspired me to start a biology talk show at my university’s radio station, titled ‘Disentangling the Bank’ for the iconic concluding paragraph of Charles Darwin’s On the Origin of Species. It’s a one hour program where two co-hosts and I summarize papers we found interesting that week and talk about the major results and implications. Because of your thorough preparation I’m always telling them to go to the primary source, much to their chagrin. We can’t go as in depth as your show, not only because we lack the knowledge which comes with being in the field for years, but also because this show is aired live to the public. This results in us heavily summarizing each paper. Nevertheless, we have a great time discussing the articles off-air in depth and it has become a sort of running joke that I always have a microbiology paper each week (never taken from your show though). Keep up the great work and thanks for the inspiration.


TWiM 70 Letters

Jim writes:

Just heard TWIM 67 -- excellent of course -- and recalled, like Elio, being in basic training in the 60's when meningitis cases occurred on the base and we had to sleep with all the barracks windows open. I think we were double-bunked but can't recall if we slept head-to-foot, or if adjacent bunks were reversed. It was a cold time of year and open windows didn't improve the experience, but it seems like they were closed after a couple weeks.

Smithfield, VA

Richard writes:

Good morning, day, evening (depending on your time of day). Esteemed

Firstly my weather report, for Weston super Mare, uk.

It is currently 3 centigrade (feels like 2C), dew point 4C, humidity
78%, there has been 1mm of rain/sleet, with a 50% chance of further
precipitation, and the wind is 16 km/h from the WNW. It is currently
dark so no visibility, but this is estimated as 2 miles, as it is
cloudy with light rain.

The predicted high for the day (2PM) 9C, with humidity of 68%, and dew
point of 4C, with predicted wind of 21km/h, a 40% chance of
precipitation (rain or sleet), to is expected to be partly sunny, with
good visibility >10 miles predicted.

I hope the weather report meets your increasingly exacting requirements :)

My question is actually fairly simple; Giardia lamblia and a number of
other eukaryotes lack mitochondria. Most of them appear to be
anaerobic, and I can see the point that the mitochondria and electron
transport mechanism might well be selected against.

However, no where can I find if it is clear that mitochondria where
selected against, and lost. Or if these bugs are a branch, that where
started before eukaryotes adopted mitochondria.

I'm not scientist, but simply an interested party. I actually work as
an engineer, on sewage treatment plants. So I do get to see a lot of
bacteria, since they do all the work, treating the sewage. Given
plenty of oxygen, and the correct nutrients, they do a fine job of
this, and then happily settle out, leaving clean enough water that it
can be returned to the environment (or with minimal treatment, and
filtration, to the drinking water supply, as is becoming more

However it is my personal theory, that apoptosis in eukaryotic cells
derives from the incorporation of a once parasitic bacterium. Such a
parasite requiring a method to kill the host cell, in order to
proliferate into the medium, to infect other cells. I hypothesise that
this was co-opted by eukaryotes, in order to allow for apoptosis (or
programmed cell death).

Knowing if apoptosis occurs in eukaryotes that lack mitochondria, and
if they are a pre mitochondria branch, would answer my question.
However I have been unable to find the required information.

I wonder if you can point me in the right direction, and also thought
the subject might lead to an interesting conversation on the podcast.

Many thanks for your ongoing series of podcasts.

I have emailed this to both TWIP, and TWIM. I suspect it is better
suited to TWIM, but my research has been on parasites, since these
seem better studied, so have included TWIP.

Thanks in advance for any insights you may be able to provide, or
simply interesting conversation.


John writes:
Dear TWIMmers,

I just saw this article about the rise of drug resistance:

It seemed a bit sensationalized to me, but as far as I could tell was pretty good on the facts, and I thought it might make an interesting listener pick of the week. I'd love to hear what you all think of it.

Reading the article, I wondered what we could do to keep resistance from arising in new antibiotics. For example:

a. Could a drug company refuse to license a new antibiotic for veterinary use or for agricultural use somehow? (Ideally we would just ban mass agricultural use of antibiotics, but who knows whether that will ever happen.)

b. Could someone develop two new antibiotics with different mechanisms of action, but only sell them in a combined form? That would probably slow down development of resistance, sort of like the use of multiple anti-retrovirals in treating HIV patients.

c. Would it be possible to develop a new antibiotic, and then evolve resistant microbes and try to redesign the antibiotic to overcome the resistance? If you went through a couple of these cycles of changing the antibiotic and then evolving resistance to the new antibiotic, is it likely that would yield a final product that was hard to evolve resistance to? Or would the microbes just find a different way to become resistant?

Thanks for your wonderful podcast, and for answering my amateur questions,



TWiM 69 Letters

Gian writes:

Beloved TWiMers,

Did you see this paper in PLoS Computational Biology? It's mind-blowing. U. Maryland researchers found evidence for Acinetobacter and Pseudomonas nucleic acid integrated into human chromosomes and mitochondria, possibly causing cancer in some cases.

Bacteria-Human Somatic Cell Lateral Gene Transfer Is Enriched in Cancer Samples

Big fan,

Bard College

Robin writes:

Liquid water without bacteria on earth:

Aqueous humour
Cerebrospinal fluid
Amniotic fluid

(No mention of exclusion of biological entities.)

Ergot on the forehead: close, but no cigars!


It is used medicinally for treatment of acute migraine attacks (sometimes in combination with caffeine).



Dihydroergotamine (/daɪˌhaɪdroʊ.ɜrˈɡɒtəmiːn/ dy-hy-droh-ur-got-ə-meen; brand names D.H.E. 45 and Migranal) is an ergot alkaloid used to treat migraines.

Spores "blow in".

Bacteria, if spore-formers, may do likewise.

Tinea versicolor/pityriasis versicolor:

Recent research has shown that the majority of Tinea versicolor is caused by the Malassezia globosa fungus, although Malassezia furfur is responsible for a small number of cases.

(Mostly a cosmetic problem.)

Microbiotum & microbiogenome?

Don writes:

Greetings and the usual well earned accolades. I have a few questions about the protective effect of "melanin" in the gut on the reticuloendothelial system. If melanin ?or its precursors are truly insoluable how was the bone marrow protected? Were the mice restrained during radiation to shadow the bone marrow by the gut laden with rooms, or is a melanin precursor responsible for the remarkable effect? To have fed refined melanin instead of the Trader Joe's fungii would answer a lot of questions. It is usually the failure of the bone marrow [reticuloendothelial system] that has killed those people with radiation poisoning, and a protectant would aid such mundane efforts as a manned Mars mission. Thanks again for your gift to science.

Don Kingsley Jr, MD

Marion writes:

the letter below posed the question how do prokaryotes perform chemiosmosis with only one membrane.

two membranes are not required for proton gradient-driven ATP synthesis. proton pumps in electron transport chains in the prokaryotic cell membrane concentrate protons inside the cell. this drives membrane-bound ATP synthase, producing ATP inside the cell. in fact, mitochondria are hypothesized to have been derived from endosymbiosis of the ancestors of purple sulfur bacteria.

A perquisite of teaching undergraduates.

original email:
Nick writes:
I teach high school AP Biology and Microbiology and have a question about ATP sythesis via oxidative phosphorylation in Gram-positive bacteria (and I guess archaens, too). In mitochondria, chloroplasts, and Gram-negative bacteria, it is possible to concentrate cations (hydrogen or sodium) in an enclosed space to drive ATP synthesis through chemiosmosis. I do not, however, understand how this is accomplished in Gram-positive bacteria and have been unable to find a satisfying answer on my own. Some things I found seem to indicate that the cell wall may trap hydrogen ions (I read something about secreted enzymes not gaining function until they made it all the way out of the capsule due to lower than optimal pH levels) or that aerobic respiration only occurs at high efficiency in the deepest layers of biofilms (something about protons concentrating when the attaching surface has a negative charge), which leads me to believe that Gram-positive bacteria are indeed pumping proton
s out into the surrounding extracellular fluid in the hope that they can be used before they diffuse away.

Greg writes:

Dear TWiM hosts,
The last few episodes have been great as usual. I wanted to comment on two things.

1. I feel that the term "microbiome" should refer to the set of microbes living in a given environment. It seems to me that there needs to be a term for this idea in any case. As for the set of genes or genomes present in a given sample, am I wrong in thinking that the word "metagenome" is adequate for this? Besides, what exactly do we mean when we add "-ome" to the end of a word? A genome is a set of genes (well, sort of). A proteome is a set of proteins. It seems logical that a microbiome should be a set of microbes. We have the added bonus that a microbiome can also be a biome. I don't know, but perhaps the word was even used in this sense before everyone started overzealously adding "-ome" words to our, um, word-ome.

2. The story from TWiM #67 about melanin-containing fungi living in environments with a lot of ionizing radiation was indeed fascinating, but I am inclined to feel skeptical about the idea that these fungi are actually deriving energy from that radiation. Is there any evidence that the fungi harness the energy of ionizing radiation? I am neither a microbiologist nor a nuclear physicist but my first guess would be that the fungi are merely unusually resistant to radiation - perhaps they are very good at repairing damage to their DNA. This resistance would allow them to thrive where other organisms can't, even while using conventional sources of food. Although I can't say I understand photosynthesis, my impression is that there is a good understanding of how the energy of visible light can be harvested by chemical means. The energy of visible photons must be a good match to the energy of a useful transition between states of a molecule. Of course, ionizing radiation also couples to chemical changes, since it can blow molecules apart, but is there any way to capture the energy when this happens? I haven't heard of anything like this. It is worth finding out, but as Carl Sagan said: "Extraordinary claims require extraordinary evidence."

I am a great fan of TWiV, TWiP, and TWiM. Keep up the great work!



TWiM 68 Letters

Dr. Robert Kelley writes:

Dear Twim Docs,

I just finished listening to the latest episode it Twim on the microbiote's effects on obesity. There was discussion about the use of donor feces in the treatment of human disease. I thought this might be of interest.

Harnessing the Healthy Gut Microbiota to Cure Patients With Recurrent C. Difficile Infection

This study is currently recruiting participants.

Love the show.

Yours truly,

Robert Kelley, Ph.D,

Nick writes:

I teach high school AP Biology and Microbiology and have a question about ATP sythesis via oxidative phosphorylation in Gram-positive bacteria (and I guess archaens, too). In mitochondria, chloroplasts, and Gram-negative bacteria, it is possible to concentrate cations (hydrogen or sodium) in an enclosed space to drive ATP synthesis through chemiosmosis. I do not, however, understand how this is accomplished in Gram-positive bacteria and have been unable to find a satisfying answer on my own. Some things I found seem to indicate that the cell wall may trap hydrogen ions (I read something about secreted enzymes not gaining function until they made it all the way out of the capsule due to lower than optimal pH levels) or that aerobic respiration only occurs at high efficiency in the deepest layers of biofilms (something about protons concentrating when the attaching surface has a negative charge), which leads me to believe that Gram-positive bacteria are indeed pumping proton
s out into the surrounding extracellular fluid in the hope that they can be used before they diffuse away.

Microbiology is not my native discipline, but I have become enthralled (in no small part due to the TWi family of podcasts) as I try to both improve my Micro course and interject a healthy respect for our evolutionary forebears into the AP Bio curriculum. Any additional information you can provide would be greatly appreciated.

Thank you,


Jim writes:

Hi Folks,

Just to pound on an older discussion topic of hand sanitation here's a link to a recent study that shows gloves didn't help reduce MRSA and VRE infection, link.

Smithfield, VA

Jim writes:

Thought this site, livingto100, might be of interest, perhaps to listeners as well. I expect only another 10 years, at best, and now apparently will make it to 97! Hah!

Smithfield, VA

Greg writes:

Dear All,

I have three brief responses to TWiM #66:

1) I always enjoy the episodes with all four of you best of all. Every episode is good, but the ones with all four are especially a treat. Thank you.

2) With regard to the subject of what should be meant by "microbiome," I think that the word should refer to the genes, rather than the organisms, in a given environmental context. I do not think that this is what the word currently does mean, but that is what it should mean. There are two reasons for this. First, as Elio noted, the term is currently redundant over "microbiota," and there is nothing gained by having two words that mean the same thing. The second reason is more complicated. Basically, it seems to me that it is possible for the word "microbiome," considered as a catalog of organisms, to become meaningless when pressed too far. That is to say, E. coli K-12 and E. coli O157:H7 are very different organisms. The former has ~4.3 x 10^3 genes, while the latter has ~5.4 x 10^3. Nevertheless, they both classify as "E. coli." This means that, when one speaks of the "microbiota" as a sort of catalog of the different species that live in a given environmental context, one elides over a lot of the diversity that is found there. To speak of molecules instead of organisms avoids this problem. Therefore, it is simply more useful to make the term "microbiome" refer specifically to molecules instead of microorganisms.

3) Michael has a good point about the need for a word that covers both the microbial and the host molecules that interact with each other, but this concept needs its own third term. Assimilating this third meaning into the already confused term "microbiome" would only further tangle up the mess that Elio is rather conscientiously trying to untangle.

Every episode is a treasure. Keep up the good work.

Andy writes:

To my valued friends at TWIM:

Having recently read a Watson book on DNA history, I was reminded of an old TWIM episode that included an 'old timer' who gave numerous stories about his work at Woods Hole and Cold Springs Harbor. The episode may have actually taken place at Cold Springs.
Even though I could tell that the history being related during this episode qualified as 'precious', I was clueless. Now, having read this book, I would give my right arm to hear this gentleman tell his stories about these labs in the 50's, 60's and beyond. But…I can't find the darn episode!!! Can you please help?!? I will send you my right arm!

your avid fan and listener, Andy

P.S. it's my own fault of course that I don't have ALL your episodes; most of them continue to fill up my phone and laptop and always will. I realize I can access the few that I reluctantly deleted. Isn't it a law that I would be looking for the rare deletion…

P.P.S. I will spare you the hearty approbations that your show deserve; you must get those all the time. TWIM gives meaning to my life! literally, I guess.


TWiM 67 Letters

Jim writes:


The last 10 minutes or so of the Mike Tech Show podcast 447 covers Mike's music collection of some 30K tracks and he may have everything Frank ever did. He is linked to the Apple music system and your daughter might be able see what he has, etc. Just a thought. Plus he discusses some useful apps she/you might use, if not already using them.

Smithfield, VA

Jim writes:

This link from quora asked the question in the subject and includes many comments I found interesting. Your listeners might be interested?

Smithfield, VA

Kehaulani writes:

Aloha TWIMsters;
I must start by saying that I love your podcasts and have been listening since TWIV day 1 (really) and thank you so much for providing such and informative and entertaining discussion on the issues related to microbes. I just saw this article, A Case Study of Gut Fermentation Syndrome (Auto-Brewery) with Saccharomyces cerevisiae as the Causative Organism, referred to in the news and had to send it to you for comment. The authors conclude with a message to health care workers that treat patients for alcohol intoxication that claim to not have been drinking and how this condition can have serious social costs if misdiagnosed. I wonder if this condition is more prevalent than we realize due to the increase in a diets high in sugar and carbohydrates as well as the use of antibiotics that disrupt the gut biome, which allows the overgrowth of this commensal yeast. I guess it gives new meaning to being addicted to carbs :)

B. Cordell and J. McCarthy, "A Case Study of Gut Fermentation Syndrome (Auto-Brewery) with Saccharomyces cerevisiae as the Causative Organism," International Journal of Clinical Medicine, Vol. 4 No. 7, 2013, pp. 309-312. doi: 10.4236/ijcm.2013.47054.

Ralf writes:

Hello TWIM,
the brain microbiome paper you discussed seems to have been largely ignored by the press. However, Mark Pallen sent you an open reply where he was dismissive of the claims of the paper, comparing it to elusive XMRV and arsenic life. He also says effectively the authors didn't do their homework.

If you can't find his letter in your mail here is the link:

I am writing because I strongly disagree with Pallen's opinion and would like to see your opinon on Pallen's letter. Indeed, I think the authors went to great lengths to get the result using different methods. And they have cultured the critters, read the part where they inoculated the mice with heated and non-heated brain tissue.The only way this could not quite be what it seems is that the bacteria are not in full bloom but dormant, like M. tuberculosis sleeping in macrophages. Low transcriptional activity they have found actually supports this hypothesis.

I'm a former biocurator who only did a bit of library work on M. tuberculosis, so that paper rang a bell with me.

Many thanks for your work and for bringing up that paper which probably has sparked some frantic activity by now I'd guess...

Regards, (and check the citation below)
Ce sont les microbes, qui auront le dernier mot. (Pasteur)

Tim writes:

Dear Vincent & Michael,

In TWIM 64 the episode on URI & UTI you and the guests get on the subject of agriculture and antibiotic resistance in microbes around 56 minutes into the video. Michael mentioned that manure is suppose to be heated before application to fields and indicated its not and if was it wouldn't be sufficient to destroy DNA which I'm assuming he meant plasmids containing resistance genes. I know it wasn't the focus of the show and time didn't need to be devoted to fully discussing the roles of animal agriculture and manure in microbial resistance but I feel there may be some clarification needed. Manure lagoons were discussed in which case we are talking liquid manure and not something you'd apply to land growing crops for human consumption. I'm sure it's legal in the case of a sufficient waiting period from application to planting although I'm not very versed in the exact specifications as I'm a dairy farmer not a vegetable grower. By heating I think Michael was referring to composting of manure. This is a process that in the case of organic farming and I'd assume conventional as well is supposed to be carried out with strict controls involving temperature measurements and records along with scheduled aeration and the like to make a product allowed for use in human consumption crops. There is a lot of interesting research out there on prevalence of antibiotic resistant genes on farms, in manure, in soils on farms, and comparisons of different operations. This could be a possible future episode for you in an area you usually only dabble in on occasion, that being agriculture. Here are some links to papers I could find on the subject I've found interesting:

I could go on for hours about this subject and its implications for agriculture and society as a whole but I need to get to the farm milking. Have a great day.

Tim Zweber
Zweber Farms

Kehaulani writes:

Aloha TWIMsters,

Just wanted to thank you for all the work you do bringing the world of microbes to the masses ;)

As a student in Microbiology, I listen to all the TWIx podcasts and enjoy them all :) Last year, I wrote a paper on the gut microbiome and came across a paper that might identify a causal agent in obesity (citation below). I am not sure why it did not get the attention (both media and scientific) that the paper you discussed this week since it seemed to be similar in focus. It seems that inflammation plays an important part in obesity and the presence of the bacterial toxin might be the culprit. The researchers concluded that endotoxin-induced inflammation might have a pivotal role in obesity (as induced by the bacteria E. cloacae strain B29). The man in this study lost weight when switched to a whole grain diet with probiotics and the bacterial strain was undetected. I wonder if the paper you presented obtained a similar result in mice fed a low fat diet where the gut microbiome contained a healthy diversity. There have been many studies that show a diet high in fat and sugar contributes to obesity, but could it also maintain an unhealthy gut microbe that could produce an endotoxin that stimulates inflammation? In the study you mentioned that the diet was important in maintaining a healthy gut diversity. I guess this means that the use of any prebiotic for weight loss would be meaningless if not accompanied by a low fat diet? How does this explain those that are thin and eat an unhealthy / fast food diet? I know this is a complex issue but I can't help but think of the effect of an endotoxin producer and resulting inflammation as a likely culprit in obesity. I feel for those that have been frustrated by the "calories in = calories out" statement .. these studies show that it is not that simple.


Na Fei, Liping Zhao, 2013. An opportunistic pathogen isolated from the gut of an obese human causes obesity in germfree mice. ISME J. 2013 April; 7(4): 880–884. Published online 2012 December 13. doi: 10.1038/ismej.2012.153


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