TWiM 39 Letters

TWiM 38 Letters

TWiM 37 Letters

TWiM 36 Letters

TWiM 34 Letters

Dear TWiM Team

I see that some action is now being taken in America against the non-therapeutic use of antibiotics as livestock growth promoters:

http://www.nytimes.com/2012/04/12/us/antibiotics-for-livestock-will-require-prescription-fda-says.html?_r=1

http://www.fda.gov/NewsEvents/Newsroom/PressAnnouncements/ucm299802.htm

Having read the FDA Press Announcement I think that that the N.Y. Times article may be misleadingly optimistic, I feel that this is probably too little and too late.

The practise of using antibiotics as growth promoters was stopped in Sweden in 1986 the UK in 1988 and in Europe by 2005, without significant adverse effects on the meat industry.
As I see it the only reason this practise persists in America is the lobbying by the livestock industry against the scientific consensus.

Your views please doctors.

Peter

Article about how use of AGP's was phased out in the Danish pork industry:

http://www.thepigsite.com/articles/2/ai-genetics-reproduction/1735/danish-pork-industry-antibiotics-prohibited-as-growth-promoter-part-3

Antibiotic Growth Promoters in Agriculture: History and Mode of Action:

http://ps.fass.org/content/84/4/634.full.pdf

History of the Use of Antibiotic as Growth Promoters in European Poultry Feeds:

http://ps.fass.org/content/86/11/2466.full

Sergio writes:

I have a question for Michael Schmidt. While doing my research on R. solanacearum, I read an old paper where they mentioned that Pseudomonads were able to internalize copper and therefore detoxify a copper rich liquid medium, I have observed this myself with the R. solanacearum strain I was working with, but since Michael is the copper expert in TWIM, I would like to know if there is some more new information about this phenomenon. It is of my interest beyond my doctoral thesis because copper is one of the few fungicides allowed to be used in organic farming. Therefore, this phenomenon deserves more attention from organic farmers, I think.

Sergio

Ph.D. in Biocontrol Science
Tokyo University of Agriculture and Technology
United Graduate School of Agricultural Science
Biocontrol Science Department

Instituto de Investigaciones Fármaco-Bioquímicas
Miraflores
La Paz, Bolivia

Sarah writes:

Dear TWiM-ologists,

You know how sometimes you run across a word or phrase which sounds like it's got a specific meaning that's really important to the context of whatever you're reading or hearing?

Well, I've been catching up with episodes 27-29 lately, and true to TWi form, the phrase "type III secretion" got the gears crankin'. The phrase sounded significant but I didn't remember learning about secretion mechanisms under this framework in undergrad 10 years ago. I did a little reading and wanted to share how fascinating these mechanisms are and how relevant they seem to be for many common human pathogens. Depending on the bug, the product, and the environment, these guys can deliver a variety of toxins into the extracellular environment, spit out antibiotics and other compounds, or deliver proteins or nucleic acid directly into target cells via injection or vesicles. What a spectacular array of intricate and elegant mechanisms - as Dr. Schmidt would say, "Remarkable!"

It's fitting that these podcasts are award-winning. They always nurture curiosity and prompt trains of thought into unexplored territory.

The discussion about TUNEL and apoptosis in episode 29 reminded me of a suggestion for pick of the week - A couple of music videos that Roche released in 2009 to promote some new lab tools to measure viability and cytotoxicity. They're more for tissue culture than microbiology, but hilarious nonetheless.

http://roche.cnpg.com/video/flatfiles/843/
http://roche.cnpg.com/video/flatfiles/771/
(in case the above links don't work: http://www.roche-applied-science.com/usa/celldeathtour/)

Stephen writes:

<http://ksjtracker.mit.edu/2012/05/16/twim-32-a-microbiology-chat-with-monolakian-arsenic-buster-rosie-on-scientific-error-sci-journos-and-a-submission-to-science/>

Horizontal transfer between blogs.

TWiM 31 Letters

Dear TWiM Team

A fascinating article from New Scientist this week.

Standard medical teaching is that the foetus is sterile and that the microbiome only begins to develop post natal.

New research from Spain indicates that the microbiome starts to develop before birth:

http://www.newscientist.com/article/mg21428603.800-babies-are-born-dirty-with-a-gutful-of-bacteria.html?full=true

"Pilar Francino and her colleagues at the University of Valencia in Spain collected and froze the meconium of babies from 20 women. They removed the outer layers of each sample to rule out any bacteria picked up after birth, then looked for bacterial DNA.

The team not only identified bacteria in the babies' meconium - which before then was thought to be sterile - they found bacterial communities so developed that they seemed to fall into two categories. Around half of the samples appeared to be dominated by bacteria that produce lactic acid, such as lactobacillus, while the other half mostly contained a family of so-called enteric bacteria, such as Escherichia coli."

Peter writes:

Dear TWiM Team

There was an interesting article in the March Scientific American on long term effect on health that food poisoning can cause:

http://www.scientificamerican.com/article.cfm?id=food-poisonings-hidden-legacy#comments

New studies by scientists in several countries show that food poisoning rather than lasting just a few unpleasant days can in some cases cause life long problems.
Though this possibility has been known for some time the recent work indicates that this phenomenon is much more common than previously thought.

"A survey of 101,855 residents of Sweden who were made sick by food between 1997 and 2004 found, for instance, that they had higher-than-normal rates of aortic aneurysms, ulcerative colitis and reactive arthritis."

"...several years after a 2005 outbreak of Salmonella in Spain, 65 percent of 248 victims said they had developed joint or muscle pain or stiffness, compared with 24 percent of a control group who were not affected by the outbreak."

Peter

PS I that the Scientific American journalist and author Maryn McKenna would be a good guest for TWiM or TWiV.

Nathen writes:

Hey thanks for the great podcast. TWiM is one of my new favourites. (I'm about to post a review on my blog.) I'm a little afraid to start listening to TWiP and TWiV--if I get hooked I'll never be able to keep up with all of them.

I just listened to your episode that included the paper on the autism microbiome study, and one of you said something about it being difficult to recruit controls for this kind of invasive procedure. It might make the statistics more complicated, but what about recruiting siblings of autistic kids as controls? The parents would be much more likely to be on board, as they have a vested interest in the progression of science on the problem of autism.

Thanks again,

Nathen

Steve writes:

Hello Vincent and cast of TWIM;

I have to say, even though I am a novice, I really enjoy your podcasts.

Because of the nerdy-ness and nature of this song, I thought I should pass it along. Happy St Patrick's Day! Enjoy!

http://www.youtube.com/watch?v=L6dzUOYTQtQ&feature=channel

TWiM 30 Letters

Megan writes:

I am a Clinical Microbiologist, and have really been enjoying the insights and discussion on TWIM and TWIV (and am hoping to get to TWIP soon). I have really found the information being presented helpful, and am wondering if any of the lectures from the hosting professors are available online. I have found some of Dr. Racaniello's lectures in the iTunes store, are any of Dr. Schaecter and Dr. Schmidt's lectures available online?

Thank you for any information, and thank you for the valuable resource you are providing with these podcasts.

Dallas writes:

Being a retreaded physics/physical chemical/thermodynamic type without any formal education in biology of any kind, I find your podcasts accessible -- even if somewhat hard to get my mind around.  Your are good about defining the jargon that exists in every field of science.  

I have spent 35 years working in aquaculture (the raising of aquatic animals) in systems whose real performance is controlled by the microbiologic ecology.  In my sub-field of recycle aquaculture, I partition this microbiological ecology into separate unit operations like biofilters, where the performance is a little more controllable/predictable, but still would have a metagenomics as complex or more complex than the human gut.  I have seen very few papers even attempt to get a handle on these complex system.  

In the practical microbiology department, I have developed a series of fluidized bed biofilters that are able to remove some hazardous materials from ground water down to non-detetable levels of < 1 ppb, well below the minimum substrate concentration for the bugs of about 20 ppb.  In particular MTBE , a water soluble gasoline additive, enters ground water from leaky underground storage tanks and people can taste it at 50 ppb.  In Calif. the political class went ballistic over this minor contamination problem and forced a multibillion dollar solution, which means that gasoline is 50¢/gal higher in Calif that the rest of the country.  The political class supported by the press was going on about how MTBE was non-biodegradable and the lawyers were making a fortune.  

My experience indicates that very few chemicals are non-biodegradable, if there is energy that a bug can obtain from degradation.  If that weren't true, we would be up to our eyeballs with all sorts of refractory organic chemicals.  

I heard that UC Davis and UC Riverside researchers has some very slow growing bacteria that seemed to metabolize the MTBE and they were digging up all sorts of leaky underground tanks in my area.  Knowing that these bugs had a 10+ day or so doubling time combined with a 10% or so yield, I knew that I had to setup a reactor that could maintain the bacteria while processing large volumes of liquid over very long time periods.  It took me 9 mo to get my first bioreactor running using seed from the universities, sewerage plants and every soil around a leaky tank I could find and a continuous feed of MTBE as the only energy source.  I ended up making some money growing kg amounts of these bacteria consortia attached to sand grains used to as seed to start up new bioreactors on new sites and went through many bbl of MTBE growing and feeding them.  We can go into a bioreactor at 2000 ppb and come out at < 1 ND with a 15 minute contract time.  

The trick of obtaining a continuous discharge concentration below the Smin (minimum substrate concentration for the bacteria to break even -- zero net growth) is to have plug flow on the liquid phase of the system and mixed flow on the biological phase.  You fatten up the bugs in the bottom at a concentration above Smin and they keep eating when they get moved to the top where the concentration is below Smin.   If the inlet concentration gets near Smin, we have to add MTBE to the input water to maintain a lower discharge concentration.  Try telling a regulator that you are going to add a pollutant to the water to get a lower discharge concentration and it blows their minds.

The concept of these fluidized bed bioreactors could be an interesting research tool for the dental bugs you have mentioned.  You could fluidize small grains of tooth enamel, where effectively every small grain is in free fall in the culture media all the time, and you could see what happens to the consortia as you change the feed composition -- coke vs pepsi vs apple juice vs mouth wash, etc.  

Continue the good work.  

Dallas

David writes:

Dear Professor,

I am a former molecular immunologist who now works as an attorney doing catastrophic birth injury defense.  I can't thank you enough for enriching my drives with TWIP, TWIV, TWIP and TWIM.

As you can imagine, one of the bugs which occupies a lot of my thoughts is GBS and its proclivity for vertical infections of fetuses.  I know that in a certain percentage of individuals are colonized and happily walk around with GBS never causing a problem.  What I would be really be interested in learning more about is what can make happy colonizers into pathogens.  My thought was that perhaps in fighting for territory a bacterium like GBS expresses virulence factors which, in some conditions, allows it to crowd out other flora.  Some sort of swarming like event gets it to spread out and it encounters the fetus.

I know this is likely a gross simplification- but if you have any ideas or suggestions for reading I would be in your debt.

Once again- many thanks for the hours of fun.

Nathan writes:

Hi TWiM-ers,
I have not listened to every episode of TWiM yet, so you may have answered these questions already. If you haven't, though, will you address these two?

What do you think you do differently in your non-professional lives because of what you know about microbiology?

Describe exactly what it takes to create selection pressure on microbes. I'm thinking about the mainstream conversation around microbe-specific antibacterials vs. alcohol-based sanitizers vs. regular soaps, but I'd like to know the general principles with which you approach that line of thought.

Thanks!

TWiM 3 Letters

Hello Professor,

I'm a Belgian student in veterinary medicine (I hope my English isn't too bad), and I'm very interested in microbiology. I have a few questions about the last episode of TWiM (and quite a lot about episodes of TWiV, but I'm still in the process of listening to all of the episodes first in order to be sure answers aren't already discussed) :

The first questions are about the Yersinia Pestis infection story : during the explanations about the life cycle of Yersinia, you talked about iron as the main limiting reagent in many infectious processes. Is it only because of the fact that it's not easily available in the host, or is iron a more important reagent than other trace elements like Zinc of Manganese? Also, are the requirements for such reagents the same in bacteria as in eukaryotic cells? I suppose not since there are already some variations among domestic animals, but in that case are the differences important?

The other question is about the microbiome. You talked about the NIH microbiome project and studies about bacterial microbiome. Is there a similar project about a viral microbiome going on?

Finally, could you make an episode about bacteriophages and their relations with bacteria, and phagotherapy?

Thanks a lot for all your podcasts and blogs, it's really informative and feeds my passion for microbes more and more. Keep up this great work!

PS : I plan to do a PhD in microbiology after I get my diploma, but I hesitate between bacteriology and virology, both are so fascinating. How did you choose your area of research, and do you have advices to choose between one or the other?