Viruses

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 4 Letters

Aric writes:

I just stumbled upon your podcasts last week and wanted to say that I enjoy them all (TWiV, TWiP, and TWiM). While listening to episode one of TWiM I began to think about the significance of finding human DNA in a bacterial genome. While this discovery is certainly very exciting I do have one question, doesn't the nature of LINEs make this discovery somewhat less remarkable? They are reverse transcriptases, which are built to copy and insert themselves into host DNA. I think this discovery may be due to the fact that LINE elements are very mobile sequences, and N. gonorrhoeae may be the 'victim' in this case. What are your thoughts on this? And would you feel different if the DNA found in the bacterial genome contained a gene for a membrane protein (or other random human gene) instead of a LINE?

-Aric

Allie writes:

TWIV, TWIP, and now - of all things TWIM? it just doesn't get any better. As an adult 'back to schooler' and beginning-again science learner, I can't believe my luck at beginning my ed adventure into science and beyond, during the era of the "Axis of unsee-able"  - the TW's. Once I listen to a TW discussion, the book (especially those dratted ch's on microbe-human interactions and all the replication stuff - aarrggh) comes alive. Here I was last week wishing you TW guys had a microbiology podcast, and poof - my prayers are answered! I thought my ears would pop out of my head as I listened along to TWIM #1, and actually understood stuff! This makes learning fun! You guys have a somehow magical combination of hard-core geek-ism, humor, loopbacks to clarify things for the "LlL's" (less learned listeners), and way too cool: all the heavy hitters seem to be gettin' together to chit chat - thanks a 10(-)7th mol or something like that (clearly more to learn!) Let's vote you folks along with  Sal Khan as "egalitarian educators" of the year(s)..

(by the way the piece of human DNA stuck in there on Ng thing was really "eerie", as Sal Khan of Khan Academy would probably say. And, the copper thing - why can't microbes eventually get around that, like they get around everything else eventually  - temp, salinity, pH, penicillin? Years from now I'll realize this was a dumb question, but for now it has Viagra me wondering).

Thanks

Allison

Kenneth writes:

Hi Vince, was just about to download TWiV when I saw that you have actually released the first episode to TWiM on the microbeworld website and I just can't stop jubilating. I strongly hope this podcast would be successful as TWiV and TWiP and I appreciate your help very much Vincent..You really helping some of us and I just cant thank you enough.

I pray for long life, happiness and good health for you, your family and all your friends helping you out to bring such an imparting tool in our lives and you all will be blessed anytime someone listens to any of your wonderful podcasts. This is just a thank you message and my questions will be following next.

All the best and goodluck.

Best Regards,

Ken (BioCrowd) in case you've forgotten me.

Stephen writes:

Here's a couple of ideas for signing off the show: "Another TWIM is added to the culture." "Another TWIM enters the culture." - Stephen

Atila writes:

Dear twimers,

First of all, congratulations to professor Racaniello and Racaniello Media Corporation for this new initiative. I am a regular TWiV and TWiP listener from Brazil, and just when I had listened to all episodes, you release this new podcast. Now I can only expect This Week in Vertebrates, or This Week in Plants. Until then, let me make my first TWiM question:

Many times I have heard the explanation that the smell that comes after the rain is caused by antibiotics produced by actinomycetes and other bacteria in a silent war for space. But I have never seen a decent reference to support this. People always say it but do not cite any source. Is it true, and do you have a good source for this?

Thank you all for making another fantastic podcast. I hope you inspire other researchers to do the same, or else Racaniello corp. will end up having 10 or more podcasts, and this is monopoly! Best, Atila Iamarino

p.s. thanks also for introducing Futures in Biotech, its a great podcast too and I am impressed. I'm listening to old episodes, from 2006 to 2008 and many of the discussions are about research that I have only heard last year. I'm anxious to get to the new episodes and know what will be published in 2015.

TWiM 39 Letters

Merry writes:

Writing the sprint event for the Microbial Olympics published recently by Nature Reviews Microbiology was surely my most fun writing assignment ever! The idea for this feature article originated with Dr. Andrew Jermy, Senior Editor at NRM in London back when the city was just starting to hum with preparations for the summer Olympics. He invited Forest Rohwer and myself to cover one of the events. Fortunately he offered us the sprint, which was a perfect opportunity for my favorite entrants, the phage, to win. He also enticed me by clearly stating his intent, that this was to be a fun piece for the reader (and the authors alike). Because my name happens to be first on the article, rumors have been going around that this was my idea. Actually, this was but the latest of a series of innovative features he has put together. I look forward to the next one.

Merry Youle

James writes:

Hello twim,

I just wanted to write to you guys and say thanks for highlighting our nature reviews article (Microbial Olympics). I'm glad our approach of writing a pieces that could be appreciated by experts and laypersons alike was successful and as its my first outing into the publication world I'm thrilled it has received such positive feedback! Thanks again!

Sincerely

James Gurney

Jim writes:

Another wonderful TWIM.  
Jo Handlesman's credentials are more impressive by the week.  

Will apologize for my low brow humor in the letter you read.

Taking a dump is used to say having a bowel movement. Hence "dump data" would be data derived from the study of bowel movements.
73

Stanley writes:

So, maybe it was because I was irritated from sitting in a traffic jam in LA, or maybe (like Elio) I was just being an old curmudgeon. As I was parked on the freeway listening to TWiM and looking forward to accelerating through Elio and Michaels autobahn through the recent General Meeting of the American Society of Microbiology, their comments made me feel stuck in an intellectual roadblock.

Elio made a good point that when a field gets started it begins with a lot of ideas, then goes through a period of accumulating a lot of data, before finally maturing into a robust blend of ideas, data, and broad insights that lead to interesting, testable predictions. But research on the microbiome is not just stuck in the boring burial in data phase. The field began with learning about a small number of cases to learn "who is there" and trying to guess from the sequences "what are they doing", work that was important to build the foundation of microbiome studies. And, it is true that there is a lot of that still going on in labs around the world. But the research has also progressed to other broader questions like how does the microbiome change after treatment with antibiotics and how long does it take to recover, how does diet influence the microbiome, is a person's microbiome stable or does it change over time, do certain microbes in the microbiome seem to protect against particular diseases -- questions that both make us think about the role of microbes in our health and illness, and data that leads to testable predictions that can lead to new therapeutics and treatments. For example, probiotics have been around for a long time, but we didn't understand how they work (and in some cases didn't even have good evidence that the really do work). Likewise for age old treatments like fecal transplants.

In short, this is a very exciting time for the microbiome and, if you're willing to listen and think, a fun time to be in the audience learning about the new Generic Viagra discoveries. If you'd like to hear from some of the people who spoke at the ASM as well as some perspectives on the future of this work, check out the ASM Life interviews from the General Meeting (http://www.microbeworld.org/index.php?option=com_content&view=article&id=1204).

Thanks for the cerebral distraction from the bumper in front of me. --> Stanley


Joe writes:
I wanted to follow up to an email the I sent to you all a while ago about evolution and entropy and my sense of paradox  regarding the ever increasing complexity of biologic systems and their concentration of energy in spite of the overriding  natural continual dispersal of energy captured in the idea of Entropy.

Let me first say that one of my gifts as  a scientist and engineer is an ability (and willingness) to ask fuzzy questions about bigger concepts at the boundaries of my knowledge looking for unexpected insights. Usually these questions are not quite so fuzzy that I mistake 2 for 3 as in the laws of thermodynamics, I guess I just like Gibbs Free Energy more than Entropy! That effort to identify what we don't know that we don't know is what has always excited me about science, the chance to think an entirely new thought that reveals something new about nature. How cool is that!

I appreciated that Michael and the rest of the crew tried to tackle the question in the spirit that it was offered and his answer essentially pointing out that nature arrives at complexity through massively large numbers of trial was useful after I thought about if for a while. Yet I must say that it still did not quite get at the core of my question. I was surprised by the email responses to my question that you later read. Particularly by the person who all but accused me of being an evil Creationist! I will just say that since it is not an issue that I care about I suspect the assertion says more about his world view than my own. The phrase "evolution driven by random chance" has never seemed to capture the awesome  sense of inevitability and thoroughness that I see in evolution. To me that phrase seems equivalent to calling it "magic".

Since then, I have come across a much more complete answer to what underlies this drive to complexity in Ray Kurzweil's book The Singularity Is Near, which I recommend as an interesting read whether you agree with his thesis or not. On page 85, he references research done by Stephen Wolfram on Cellular Automatons. This is a mathematical study that describes how complex non repetitive patterns can be generated from digital systems with a few very simple rules. In particular there is a category called class 4 automata that appear to characterize the evolution of biological systems. I have picked up  Wolfram's book A New Kind of Science and even though I am but a few pages in, it appears to be a very promising brain stretcher. Assuming I don't injure my back lifting it, I will let you know if it addresses my questions about the underlying drivers in evolution.

In closing let me say that I appreciate all the great work you all are doing in all 3 podcasts. I value the dialog, spontaneity  and asides and believe that you all capture the emotional enthusiasm that make science such a great life's work.

Joe
EH&S Manager

Peter writes:

Greetings TWiM team

I saw these instructions on instructables.com for culturing bioluminescent bacteria from fresh sea fish and thought they may be of interest.

http://www.instructables.com/id/Bioluminescent-Bacterial-Lightbulb-Water-Polluti/?ALLSTEPS

For those not familiar with it Instructables is a very eclectic DIY site where people can publish instructions for various projects they have done.

TWiM 38 Letters

Jim writes:

As usual I loved TWiM #37. Jo Handlesman adds a lot imho.

I think Michael Schmidt meant "dump data" instead "data dump."  Apologizes to Alan Dove.

Look forward to the up coming bioinformatics guest.

Thanks a million

Tim writes:

Dear TWiMeisters,

I'm quite behind in TWiM, TWiP and TWiV, because of my exams, which is a poor excuse, I know! Anyway I just listened to TWiM #22 with Dr. Sacchetti, and thought I'd write in with my appreciation. As an RN student, I love it when your podcasts are specifically pertinent to my area of interest. In this case, hospital-acquired infections and the most common infections in emergency departments.

This was one of the most fascinating episodes yet. I was wondering though if you'd consider doing something on infection-control in a surgical setting? That is, if you had any papers on the effectiveness of surgical attire in preventing spread of infection to the patient, and/or protecting the surgical staff from the patient. Particularly, I'd be interested in hearing which microbes are most commonly found on the Online Blackjack skin or in the hair of surgical staff. I wonder if surgical infections would be similar to those in emergency departments, or if the percentages would be slightly different.

Admittedly, such an episode would probably not be of interest to many, and the literature may not even be out there. My main purpose for this email was simply to express my appreciation for everything that you do. Keep it up! Much respect to every one of you.

Regards,
Tim (Melbourne, Australia)

Alicia writes:

Hello,

I was listening to TWiM a few weeks back and, if I remember correctly, it was mentioned that it would be interesting to find someone that could discuss spirochetes with you.

I would like to recommend one of my professors, Dr. Caroline Cameron. She is Canada's Research Chair in Molecular Pathogenesis and teaches at the University of Victoria. I have spoken with her and if you have any future papers concerning spirochetes (especially Treponema pallidum subsp. pallidum or Leptospira) she would be interested in participating.

I hope you will do an episode!

Best,

Alicia

TWiM 37 Letters

Pat writes:

Hi Vincent,

I'm a regular TWIM listener and Assistant Professor at the University of Michigan in the Department of Microbiology & Immunology (I enjoyed your visit last semester).  I was also heavily involved in much of the data analysis for the Human Microbiome Project.  As I was unable to attend the ASM General Meeting, I cringed when you and your co-hosts described the human microbiome talks at ASM as being glorified data dumps (TWIM #36).  This is most unfortunate!  I was wondering whether you might be willing to have a guest, say…  me to help get the general microbiologists through the weeds.  As a former postdoc in Jo Handelsman's lab, I can tell you that I am very interested in making computational concepts more engaging and feel that we have an important job as scientists to view our research mission as part of our teaching mission.  Anyway, if you're ever interested, please know that you have a standing offer from a  microbial ecologist / bioinformaticist to help your listeners get excited about this amazing topic.

Sincerely,
Pat Schloss
--
Department of Microbiology & Immunology
University of Michigan

Mark writes:

Hello, Vincent, Michael, and Elio (and the other contributors!):  I want to thank you so much for these podcasts.  I have been having to sit around in traction for a pinched nerve a couple of times a week, and listening to TWiM enriches my mind while I feel like a science fiction character!  Better than watching television, in any case.

I really appreciate the interactions and information that are presented in all of your podcasts, but the comments on the ASM General Meeting (which I had attended, too),in TWiM 36 resonated.  The new "card" format for the posters was indeed wonderful for forgetful people like myself, and I have to agree strongly with Vincent's comment (and Elio's quite gentle criticism) of systems biology:  things are getting so complicated that few people can be generalists. I used to worry about "eukaryocentricity" in biology, but clearly I need to start worrying about "colicentricy."  I too thought that third slide at the opening session was a backgrounder for Salmonella phase variation---but decided I must not be "getting it," since the speaker was so clearly brilliant and engaged.  So a solid background becomes vital, even for MacArthur Genius Grant Online Casino winners, as our field sprints (it no longer marches!) forward!

One final thing.  I will be trying to introduce my undergraduates to TWiM in my Fall microbiology course.  The podcasts give an engaging and current "feel" for microbiology (I was going to say the "ferment" of microbiology, but I restrained myself).  While my students might not want to listen for an hour, we do discuss journal articles...and I intend to assign some of the ones you have been covering, with the relevant TWiM assigned as "background listening."  Extra credit points often focus attention like a laser, I find.

Best wishes to all, and thanks for what you do.  Hope to see some discussion of microbial endocrinology at some point?

-Mark Martin

P.S.  The human microbiome descriptions are indeed hard to follow!  I half-expect to see advertisements for entero-Harmony, the dating service that matches people based on their enterotypes.  Hmm.  What about antibiotics then?  Best wishes, MM

Spyros writes:

Hi

I heard you read my email on the last TWIM and I was super excited. Really excited.  And it looks like from the comments on the panel it's something you guys would like to pursue.  Please let me know when or if you guys get the time.

I am up to the ICAAC podcast, but i have listened ahead to the most recent ones obviously.  The podcast keeps talking about probiotics and the benefits, and I'm truly interested in them.

however I'd like to point out a recent MedWatch release and here is the link

http://www.fda.gov/Safety/Recalls/ucm311050.htm?source=govdelivery

this isn't the kind of pharmaceutical I manufacture but it's interesting nonetheless to me, and this is an example of what happens when things go very wrong in my industry, a lot of folks can get hurt, each unit is going into a person and I treat each one like a person.

Also I hope you guys mention what's going on in Cambodia, I saw 65 illnesses on CNN and no cause for it right now.  Of course that may have changed, I have had a horrendous day of travel and have been out of touch with the news, but the new can't do as good a job as you guys can discussing this latest issue.

Again thanks, look forward to hearing future podcasts and hearing from you guys.

TWiM 36 Letters

Todd writes:

Just a quick note to say how much I enjoy TWiM, and in particular, how much I enjoyed episode 32 featuring Rosie Redfield. I don't know how you find time to do this, but I'm glad you do. Keep up the great work.

BTW, I was also fortunate enough to attend the SGM meeting in Dublin in March. I enjoyed hearing you talk about the use of new media, as well as the rest of the meeting. I was also impressed at the weather they arranged for us! I entered Dublin into my phone's weather app several weeks before the meeting, and haven't yet removed it. I haven't seen a single week with weather as nice as ours before the meeting or since.

Spyros writes:

Hi

My name is Spyros and I'm a manager of a Biological Quality lab in a pharmaceutical plant.  I'm in the process of listening to all your podcasts and I really like it.  I have a Microbiology degree (Bachelors) from the University of Illinois at Urbana-Champaign, so I don't have the education of a lot of your friends / guests, but what I may be able to bring to the show a different perspective. I remember in one of the first ones, a lab tech from industry called in and asked some general questions.

I don't know if this has been brought up or were looking from someone from industry to speak on topics of pharmaceutical manufacturing and controlling flora in the environment,  monitoring we do, what we monitor, what we monitor for and general career advice.

I probably will have to work with my company's public affairs division and probably legal around what I can / can't say but I will only do that if you would be interested in having me on the show.  I don't know the exact time commitment but I will arrange to meet it if possible.  I live in free online casino bounuses North Carolina, and I know one of you regular contributors is in South Carolina, so, you would have the Carolina's covered!

I'm only on episode 6 so if you have this covered I understand.  Keep on going really enjoy the topics.

Thanks

Sarah writes:

Hi Vincent and guests,

I have been an avid listener of the TWIM/V/P podcasts for just over a year now; they help pass the time during long animal surgery hours, even longer stereology sessions, as well as during my rollerblade home from work in Los Angeles... yes I know it's dangerous to wear headphones and rollerblade in a city where people care more about the scratches on their car than a pedestrian's broken bones if a collision occurs, but hey we all have to take risks for science right?

My question is a little delayed in terms of timing; it was sparked from the January 26th podcast looking at a possible role for microbes in the onset of autism. It was mentioned in the beginning anatomy lesson that the appendix may have a role in priming the gut microbiome. I know there has been at least one study that has shown a correlation between appendectomy and an increase in heart disease in humans, and I also found a paper linking germ-free mice with an increase in atherosclerotic plaque formation. I'm curious if you or your colleagues have any postulates regarding which particular group/groups of bacteria in the appendix may be the "keystone genus" within the community- knocking them out will potentiate the results found in the germ-free mice in terms of plaque formation or other early markers of heart disease. I guess if you were going to look more closely into causal links between appendix, gut microbiota and heart disease, where would you start and why?

I hope that question made sense and thanks again for the hours of entertainment...enjoy the Spring weather!

Kindly,
Sarah

TWiM 34 Letters

Peter writes:

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 Electronic Cigarette
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

Peter writes:

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 Electronic Cigarette, 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 semenax wiki 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!

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