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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 72 Letters

Jim writes:

Hello:

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,

Jim

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” <http://www.sciencemag.org/content/341/6153/1514.full > 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

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.

http://www.youtube.com/watch?v=EFebGZ7FJQQ&sns=em

 

 

 

 

 

 

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
www.zweberfarms.com

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,

Benjamin

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.
Best,
Will

 

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.

Jim
Smithfield, VA

Richard writes:

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

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
popular).

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.

Regards

John writes:
Dear TWIMmers,

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

https://medium.com/p/892b57499e77

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,

--John

 

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

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003107

Big fan,

Gian
Bard College

Robin writes:

Liquid water without bacteria on earth:

Endolymph
Aqueous humour
Urine
Cerebrospinal fluid
Amniotic fluid

(No mention of exclusion of biological entities.)

Ergot on the forehead: close, but no cigars!

Ergotamine:

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

 

http://en.m.wikipedia.org/wiki/Ergotamine

Dihydroergotamine

 

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.

http://en.m.wikipedia.org/wiki/Dihydroergotamine

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.

http://en.m.wikipedia.org/wiki/Tinea_versicolor

(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!

-Greg

 

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,

Nick

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.

Jim
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!

Jim
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:

Vincent,

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.

Jim
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?

Jim
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:
http://blogs.warwick.ac.uk/microbialunderground/entry/the_brain_microbiome/

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:

http://www.sciencedirect.com/science/article/pii/S0160412002000843

http://pubs.acs.org/doi/abs/10.1021/ac015588m

http://www.sciencedirect.com/science/article/pii/S003807170800062X

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
www.zweberfarms.com

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.

Mahalo,
Kehaulani

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

 

TWiM 66 Letters

Neva writes:
You may have seen this. Thought you all might enjoy this header illustration from
http://blogs.scientificamerican.com/artful-amoeba/2013/08/24/wonderful-things-the-hidden-beauty-of-the-horse-dung-fungus/

All your podcast are my favorites!

Dan writes:
Hi guys,

(I should give the obligatory "love the show", but it is true: as a bioinformaticist of a fairly mathematical sort, it's nice to spend an hour a week really listening to why people care about comparing metagenomic samples, say, rather than just thinking about them as mathematical objects to be manipulated and analyzed.)

Anyhow, there was a question on TWiM about whether people wearing their scrubs home spread infections from hospitals to other environments. Vincent says people in NYC rarely wear scrubs on the subway there. Regrettably, that's not true here in Ontario. The bus I was riding while I was listening to TWiM stopped in front of our local hospital...and on came a woman wearing scrubs. And sandals!

Keep up the good work,

(here is the image)

https://docs.google.com/file/d/0B8dwAT4VdQdjS0JtZVFNSFo0WVE/edit?usp=sharing


Steve writes:

Hi Vincent,

Always amused by the repartee on your podcasts, especially towards the end; and today I particularly enjoyed the continuation of your banter over washing. It reminded me of a visit to my local hospital - a large one, serving a fairly sizeable conurbation. I had to go for an ultrasound, which was based in a far corner of the building on an upper floor. I walked all through the building, past many signs about washing hands and the need for cleanliness, and then sat down in a waiting room. As I sat there, I soon became aware of a nasty smell, and was dismayed to find I had picked up a sizeable unwanted faecal donation from what must have been a very relieved dog. With this contribution, I had left a trail of filth all through the hospital, and, if I were to get up on a gurney, I would transfer it to that - and possibly some of the staff - too. What was I to do?

As nonchalantly as possible, I removed my sandal, and found its treads firmly plugged with very sticky and smelly mess; so I went in search of a wash basin. There one was; with shiny taps (faucets), and modern scalloped basin. There were elbow levers on the taps, and a large notice on how to wash your hands... The thing was actually a safety design nightmare. The scalloped basin was shallow, and would slosh, and splash the surroundings. The tap outlets were low down on the basin and close to the sides, so you could not put anything - like my shoe - under them; anyone washing their hands would likely touch the sides of the basin. What should have been there was a deep, square sectioned, basin, with a high outlet mixer tap, delivering a good volume of water into the middle, such that hands, fore-arms, and any objects that happened to need cleaning, could be cleansed with a minimum of splashing. But, it was much worse than that. In their wisdom, no doubt, someone had decided that the public could not be trusted with plugs: but they had also decided they still wanted plugs. So they made a plug that was captive to the outlet grille; a plug that one could not take out, but which would fall in when the tap was turned on. Thus it was impossible to run something like a turd-befouled sandal under a stream of appropriately hot water, to save a hospital from the infections it carried. But my shoe *had* to be cleaned! So you can picture the scene: trying to get some water from a badly positioned tap, onto a mucky shoe, while endeavouring to keep a plug from blocking the tiny basin, without getting filth on one's self, or the surroundings! In the end there was only one way. I had to fill the basin, put the sandal in it, and scrub at it with paper towels. Then I had to put my hand in the filthy water, to hold the plug out while the water drained! Then I had to try to wash the basin; then my hands; then my hands; then my hands... Every time you wash your hands in this hospital, you either leave a basin full of dirty water for the next unfortunate, or you dirty your hands again to let the water out!

With thousands of people traipsing in and out of hospitals, without removing their shoes, - and without putting on masks, and hair covers - there isn't a hope in Hell of keeping out the germs. Without really well designed washing and toiletry facilities for both staff *and* public, there isn't a hope in Hell, of beating hospital acquired infections.

Love the show,

Best wishes,

Steve Hawkins
Luton
Bedfordshire
England
(Rather humid and sticky, after a hot sunny day.)

Chris writes:

Just before listening to the last TWiM I had finished reading <i>The Drunken Botanist</i> by Amy Stewart. It is like a garden tour of the liquor store, with history, garden tips, recipes and odd little bits of trivia.

On page 59 is a box titled "Warning: Do not add water." It then explains that during prohibition California grape growers sold bricks of compressed dehydrated grapes, with a package of wine making yeast. The label warned to not add water and the yeast, because it would lead to fermentation and that would not be legal. ;-)

This is the book's website: http://drunkenbotanist.com/

Now I am going to try to make home made homemade grenadine from page 338 from a couple of pomegranates I bought this morning.

Thanks for the entertaining listening.

 

TWiM 65 Letters

Alexandra writes:

Dear TWIM-ers,

When I began listening to TWIV almost a year ago, I had just switched majors from philosophy to biology. I am now writing to you good people at TWIM at the end of my first undergraduate summer research gig, where I have had quite a bit of fun (and frustration) mucking about with wetland bacteria. As I've been reading about all these different Bacilli, though, I've been wondering about species identification among bacteria, and about what it even means to classify bacteria as belonging to different species.

As far as I understand, most of the current work on species identification and the evolutionary history of bacteria relies on comparing the genomes of bacteria, looking for differences and similarities in highly conserved regions and in the presence or absence of accessory genes. My adviser told me that one shorthand for distinguishing between a "strain" and a species is whether or not the genomes of the two bacteria are more than 95% related to one another. This seems like a fairly arbitrary figure to me!

Then, too, some species are very closely related but lead significantly different lives, in different environments. I have had the pleasure of getting to know Bacillus mycoides this summer, but I don't think I would have been able to handle this little bug if it behaved much like its more famous and dangerous relative, Bacillus anthracis. It seems to me that any species classification must take "lifestyle" - metabolism, behavior, environment - into account.

So how do all of you microbiologists think about this notion of "species" - how do you distinguish between a genus, a species, and a strain? Is it primarily down to differences in the genome, or do you care mostly about those differences which lead to substantially different ways of living?

Thanks so much for reading!

Your faithful listener,

Alexandra

Peter writes:

Dear TWiM team I thought that this was worth a mention.

The fungus Chalara fraxinea causes Ash Dieback disease and is killing many ash trees in Britain and Europe, losses in Denmark are believed to be 60% to 90% of all ash trees.

Dr Dan MacLean, of the John Innes Centre in Norwich came up with the idea of crowd-sourcing the analysis of the fungal genome and the genomes of susceptible and resistant trees through a facebook game:
https://www.facebook.com/fraxinusgame

The hope is that the detailed analysis will give clues to the origins of the disease, and help identify fungus resistant ash trees to grow in the future.
Top gamers may have their names published in scientific articles for their role in helping analyse the genetic information. Results of the project will be made available on the crowd-sourcing website OpenAshDieBack.

More on Ash Dieback:
http://www.theguardian.com/environment/2013/aug/13/ash-dieback-facebook-fraxinus-game

http://www.forestry.gov.uk/chalara

http://www.woodlandtrust.org.uk/en/about-us/faqs/your-woods/Pages/ash-dieback.aspx

Andres writes:

Hi TWIM Team,
I love listening to all your shows TWIV, TWIP and TWIM on Stitcher Radio. Thank you very much for the many hours of entertainment and learning.

On TWIM #61 it was mentioned that the body needs gut bacteria to make vitamin K and B. If you have not had a show on these bacteria I would like to suggest that these would make a good show topic.

Keep up the great work!

Thank you,
Andy
Fremont, CA

John writes:

Dear TWIMmers,

In TWIM #61, you talked about a species of insect with a symbiotic bacteria (which itself had a symbiont), and which also had a lot of bacterial genes that had been taken up into the insect's DNA. My understanding was that bacterial DNA and eukaryotic DNA have some differences that make it hard to move between the two. Do those differences cause a problem for movement of genes between insects and bacteria? If so, is there any indication of what has to happen for the gene transfer to work, and how common that is?

At the risk of slipping into TWIV territory, it seems like these endosymbionts would provide a lot of opportunity for infection of the host cell with bacteriophage. Are there examples of phage infecting eukaryotic cells?

Thanks for answering my amateur questions, and for your wonderful podcasts.

--John

David writes:

In TWiM 60 during the email segment, there was a discussion about preservation of DNA in amber. Irregardless of Michael Crichton's book Jurassic Park, written in 1990, DNA preserved in amber has not panned out. Amber, which preserves in great detail the outer structure of insects, rarely preserves any internal material. Essentially, organisms in amber are casts. In addition, amber is porous to air, and air is corrosive to DNA. Searches for DNA in amber have not found much. Early 90's claims of DNA found in amber have been disputed. Vincent may recall my email answered on TWiV episode (I don't remember which one) about viruses trapped in amber. The article was behind a paywall so I was not able to read it, but I'm pretty sure no DNA was recovered.

FYI, DNA from bone has had more success. A recent announcement was made that DNA was recovered from a 700,000 year old frozen horse bone. So ancient DNA recovery is still possible, just not from amber.

See this You tube video by a paleontologist discussing DNA from amber.
http://www.youtube.com/watch?v=anceTKEIOXg


Christyne writes:

Dear Vincent and fellow TWiMmers,

I really love your podcast. My son told me about them, and I have worked my way through the shows. I have been learning SO much.

I recently read that children with folic acid deficiency may have a higher incidence of regressive autism, and it got me wondering about the microbiome and nutrition. I heard Michael and maybe Jo? mention that the microbiome supplies 5-10% of your calories, and I found review articles that include references for that, but I haven't found a good review of micronutrients the microbiome supplies, like the b-vitamins. Would you consider having a TWiM on the microbiome and the nutrition it supplies? Since children with autism often have problematic microbiomes, could it be that they aren't getting the right vitamins at the right times for their brain development? Can the body "ask" the microbiome for more vitamins when it needs them through signaling? Could the microbiome supply much larger amounts of vitamins than we realize? Perhaps there are micronutrients that we don't know of yet because our microbiota supply them instead of our food?

I am interested in the vitamins because of my own story. (You could leave this part out if you want to). I used to be a bioengineer working in microscopy, gene arrays and bioinformatics, but I suddenly got sick with a disabling mitochondrial disease in my mid forties. I could run a mile without thinking about it, then a year later I couldn't sit up for 30 minutes, then a year after that I was going into heart failure. I started taking very large amounts of riboflavin and my heart, which had become enlarged, shrunk back to normal size and started working just fine! Unfortunately my other muscles didn't respond so well, but I'm still alive 5 years later, which wouldn't be the case without the riboflavin. Some of my friends on my mito and FOD (fatty acid oxidation disorder) support groups are also helped a lot by particular vitamins, and it makes me wonder why did it change? I was doing fine for 45 years then suddenly I need a bunch of riboflavin to survive. I'm starting to suspect the microbiome. I like how you think about it as another organ.
Thanks for your great work! Chris

There were various review articles in pubmed related to the microbiome harvesting energy and obesity and diabetes
e.g. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3601187/

The folate deficiency in children/autism papers are sort of patchwork, but here is a sampling
http://www.ncbi.nlm.nih.gov/pubmed/?term=folic+acid+deficiency+autism

p.s. I love Elio's voice

(p.s.s. my genetic defects are normally mild ones in nuclear genes affecting fatty acid oxidation and complex 1 of the respiratory chain, so the odd inheritance and aging effects on mitochondrial dna disorders don't really apply to me)

Joe writes:

Dear TWiM folk,

Hi from Denver and ICAAC.

I'm delighted that you are finally devoting the time and attention to the most important microbiology of all--yeast fermentations.

Your letter last week from Mark on yeast inoculations reflects a very modern North American perspective on winemaking. Inoculations with clonal yeast strains are of course quite modern--wine was made for millenia without inoculation.

Many of the finest wines of France, Vincent, are fermented with their indigenous yeasts. A complex microbiome produces a more complex metabolome, unsurprisingly, giving wines of distinct complexity and subtlety of flavor. One man's complexity may of course be another's excess funk in some cases, taste is always paramount.

It is also true that choices in the vineyard may influence the success of native ferments--heavy spraying with fungicides, for instance, surely selects yeast populations. But so does weather during the harvest, tying the wine more closely to its vintage. The requirement of highly alcohol-tolerant yeast to finish the fermentations of high-sugar grapes reflects some climate change, but it also reflects a recent cultural preference in California for riper (and to my taste simpler) fruit flavors that come with grapes left on the vine later in the summer to eliminate "green" flavors and coincidentally raise sugar contents.

I hope I have the chance to wave from the audience at a live TWiM or TWiV this week, and I hope you will continue to give alcoholic fermentation the attention they surely deserve.

Best,

Joe

TWiM 64 Letters

Tim writes:

Vincent and friends,

While driving around a field cutting hay lost in my science podcast playlist the episode of TWIM #61 came up and I had to listen intently as salmonella typhimurium came up as this is a common enteric issue in agriculture. When you mentioned the work around salmonella came up with to outwit lipocalin and the idea people could in many millennia possibly evolve a second antisiderophore to combat it a thought occurred to me. Is modern medicine slowing our rate of evolution by reducing selection pressure for more fit individuals? This is not an argument for withholding medical treatments to improve the human race or something silly like that b/c obviously everyone has more important skills than the ability to fight off an enteric disease but was an interesting thought that hadn't really occurred to me before. Just wondering what you all thought of this.

Also thanks for the TWIP mention of our farm. I'll let you know if there's a TWIP bump like there is for TWIV ; )

If you decide to do an agriculture themed podcast like you and Dickson mentioned I'll be sure to listen to every episode as your opinions on agriculture are always well thought out and enjoyable to hear b/c it's interesting to see the views of very intelligent people that aren't directly in the field. Have a great day I need to get back to putting this hay down while the suns shining.

Tim Zweber
Zweber Farms
www.zweberfarms.com

Sent from mobile device w/ a small keypad, forgive brevity and typos ; )

Click to listen to this episode of TWiM (64) Live in Denver from ICAAC 2013.

TWiM 63 Letters

Hugh writes:

Hi Vincent,

I really enjoyed hearing about Carl Woese in TWiM #50. You mentioned the controversy surrounding of Woese's 1977 discovery of Archea as a third domain of life, as it contradicted entrenched scientific beliefs. Although Archea soon found its way into general scientific thinking, his work brings up another fundamental idea that is still controversial today. It relates to the word 'prokaryote.' Norm Pace, one of Woese's former students, is a strong believer that we need to stop using this word. I think he makes extremely compelling arguments about the harm this word does to basic biological understanding, and thought this could be an interesting discussion point on TWiM. Here are the the titles of two papers by Norm Pace that discuss this issue. They're both geared towards a general audience: Problems with "procaryote" (Journal of Bacteriology, 2009); Time for a Change (Nature, 2006).

I recently discovered TWiM and TWiV and am now an avid listener, mostly while cooking dinner and washing dishes, which always seems like deja vu after a long day of experiments and washing glasswear at the lab. Thank you for making that process infinitely more enjoyable. Writing from Seattle, WA,

Hugh

[we had a brief discussion of this on an early TWiM; Elio if I recall does not mind the term]

Megan writes:

Hi TWIM team,

Could you do a TWIM about the archea and viruses that infect them? It is a fascinating area that doesn't get as much attention as bacteria.


Thanks,

Megan

Jim writes:

Just another update on the hand-washing issue. This link discusses the article, which costs $10 to see at the journal.

Regards,

Jim
Smithfield, VA


Mark writes:

Hello Vincent, Michael, Elio --

I enjoy TWiM, and have listened since episode #1. Keep up the good work and keep going. Out of TWiV, TWiP, and TWiM, I discuss episodes of TWiM with my wife the most!

I am writing, belatedly, to correct some inaccuracies in episode 49 "Grape-like Clusters". These are:

1. Someone, VR?, commented that French wines were the best. This is not FACT, but a matter of taste. The Latin expression "De gustibus non est disputandum" applies.

2. Michael speculated that natural yeast was used to ferment wine. This is a common belief and is mostly wrong. There is a vigorous industry dedicated to selling commercial yeasts to winemakers. A small number of boutique wineries are experimenting with using natural yeast -- these are a minority, and the quality of their results is highly variable.

I am an amateur wine maker of 17 years. See the attached image of a macro bin containing 0.5 ton of Cabernet Franc grapes from 2012. Note the white, powder-like color on the grapes -- this is natural yeast that grows in the vineyard. Note also the stems with missing grapes -- as harvest occurs the growers typically take weekly samples to measure sugar content.

In wine making, after the crush (in which a machine separate the stems from the grape berries, and in which the berries are lightly crushed) potassium metabisulfite is added to the must (the residual grapes & juice) to kill natural yeasts and inhibit fermentation. Typically 24 hours later the must is inoculated with a yeast starter and nutrients. The image of nubile virgins stamping barefoot on grapes to make wine is, sadly, a myth.


Our winemaking group purchases yeast from a company which supplies commercial wineries, Gusmer Enterprises. Attached is their 2012 catalog. Its front and back covers commemorate scientists whose discoveries were key to wine making -- Pasteur, Leeuwenhoek, Riley, or Dewar.


There are subterranean links to virology. Vincent can speak to physicist-turned-virologist Max Delbruck and his seminal work. Did you know that his uncle, also named Max -- http://en.wikipedia.org/wiki/Max_Delbrück_(chemist) -- developed a yeast, Torulaspora delbrueckii, that will live in high alcohol levels? These yeasts are especially important in California because our climate products grapes with very high sugar levels which, through fermentation, produces high alcohol levels.

3. The paper that Michael presented provided a quantitative framework to characterize and measure the differences between grapes grown in different blocks on the research vineyard. As winemakers we see a qualitative difference in each barrel of wine. Rule of thumb: half a ton of grapes = 1 barrel = 24-25 cases of wine. It is too labor intensive to produce and label at such levels, thus wine from each barrel is blended which averages out the different tastes of each barrel.


I have TWO recommendations for listener-picks-of-the-week:

-- to learn about how a Californian coup d'etat established their wines as equals to French wine makers, watch the movie "Bottle Shock" which combines fact and Hollywood sensuality; watch the trailer here: http://www.youtube.com/watch?v=DYs0kblXToA

-- to read more about the entire process of making wines from growing grapes, figuring out when to harvest them, and fermentation I recommend the book "From Vines to Wines" http://www.amazon.com/From-Vines-Wines-Complete-Growing/dp/1580171052


In closing,

in vino veritas

Mark

PS - feel free to use the grape image. The catalog image is technically copyrighted, though I doubt Gusmer would care if you want post it.

grapes: https://docs.google.com/file/d/0B8dwAT4VdQdjRHlIdlFjdVJndVU/edit?usp=sharing

catalog: https://docs.google.com/file/d/0B8dwAT4VdQdjN3RUMHZqcjFjSmM/edit?usp=sharing

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