TWiM v3 275

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About Vincent



Thursday, 23 March 2017 18:01

TWiM 148 Letters

Written by

Sol writes:

Oh I hope I win!

I love your podcast...

I listen to all these kind of science podcasts.

Like are we there yet? Planetary radio, star talk, science Friday, etc


Dale writes:

Hi TWIM Team

I am a graduate student of medical microbiology in Port Elizabeth, South Africa.

At the moment I study antimicrobial resistance in hospital acquired infections...

Thursday, 09 March 2017 19:05

TWiM 147 Letters

Written by

Kala writes:

Dear Micro Crew,

Hello from frozen Ireland, it's 5 degrees Celsius but feels like -2, cloudy and generally miserable haha

I was wondering if you could give me some advice as I am stuck between a microbe and a hard place!

I have a BSc in Microbiology and 2 years experience working in a diagnostics lab, but I want go back to academia.

Microbiology is my passion and my lifetime love and I couldn't imagine being in any other profession. I have been toying with the idea of doing a masters in either marine microbiology or just straight marine biology. I have read up on both but I can't seem to decide which one would be better career wise...

Thursday, 23 February 2017 14:44

TWiM 146 Letters

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Jonathan writes:

Hello TWiM Team,

I'm sure it's a long shot but here's hoping for #12!

I was catching up on a SciFri podcast recently and came across this story and just had to share it with you all.  (Dr. Racaniello, I think Dixon would also appreciate this but I'll leaving sharing it to your discretion.)

SciFri: Scientific Simplicity by Design..

Wednesday, 25 January 2017 19:50

TWiM 144 Letters

Written by

Kayla writes:

Hey there TWIM team

I am a Veterinary Microbiologist in Cork in Ireland!

Long time listener of all the TWIX series and I love everyone of them.

I work in a diagnostic lab in cork and the only thing that gets me through the day is your podcasts and buckets of tea.

Thanks for the wonderful podcasts :)

Kayla ...

Wednesday, 11 January 2017 20:05

TWiM 143 Letters

Written by

Letters read on This Week in Microbiology, episode 143.

Thursday, 29 December 2016 14:21

TWiM 142 Letters

Written by

Carole writes:

Dear Vincent and hosts of TWIM,

I am a long time listener and fan of your weekly TWIM podcasts. I really enjoyed the latest episode in which you discussed a paper by Kelly Wrighton and colleagues, and was especially happy to hear you talk about chemistry! On that note I'm writing to tell you and your listeners about a seminar series entitled the Chemistry of Microbiomes, organized by the Chemical Sciences Round Table of the National Academies of Sciences. In separate workshops the series addressed Earth, Marine and Human Microbiomes, and we were fortunate to have Kelly Wrighton speak at the Earth Microbiome seminars...

Friday, 07 October 2016 02:17

TWiM 136 Letters

Written by

Steve writes:

Hi Microbophiles,

Here's an interesting little historic snippet from The Lancet.
Venerable bacteria: In another interesting history of science piece, The Lancet gets bully over Koch's bovine TB samples--but not over the tragedy of him advising that this form of the pathogen was not significant for human health, and thus delayed the introduction of basic meat and milk hygiene and testing.

It seems that the good and the great nearly always put their foot in it somewhere!

All the best,


Where it has been hot and sticky for some days (and nights: most people don't have air conditioning in UK homes.).   Incidentally: how does one get black mould stains out of pillowcases? Yes: that sticky!  :/

Anthony writes:

"The plague of 1665-1666 was the last major outbreak of bubonic plague in Britain, killing nearly a quarter of London's population.
It's taken a year to confirm initial findings from a suspected Great Plague burial pit during excavation work on the Crossrail site at Liverpool Street.
About 3,500 burials have been uncovered during excavation of the site.
In Germany, molecular palaeopathologist Kirsten Bos drilled out the tooth pulp to painstakingly search for the 17th century bacteria, finally obtaining positive results from five of the 20 individuals tested from the burial pit.
"We could clearly find preserved DNA signatures in the DNA extract we made from the pulp chamber and from that we were able to determine that Yersinia pestis was circulating in that individual at the time of death," she said.
"We don't know why the Great Plague of London was the last major outbreak of plague in the UK and whether there were genetic differences in the past, those strains that were circulating in Europe to those circulating today; these are all things we're trying to address by assembling more genetic information from ancient organisms."

Steve writes:

Hi TWiM team,

Just to say thanks for your interesting discussion of the points I raised regarding uses of gut gas analysis/fingerprinting, and hand hygiene in the context of declining use of copper coinage.

One or two of my points weren't expressed very well:

I hadn't intended to convey the sense of a general increase in the spread of infectious diseases‎, but more in the increase and spread of antibiotic resistant strains. The widespread use of antibiotics and antiseptics in hand and surface cleaners has, most likely, produced the general decline in infection that the team noted, but, previously, there would have been a good deal of copper in circulation on people's hands in addition; and bacteria on the fingers would frequently be brought directly into contact with copper metal, which would kill them before they could be passed on. This may have held back the spread of antibiotic resistance.

It does strike me, that, from what I hear in your podcasts, antibiotic resistance does not have to arise denovo very frequently: it is a part of the general  variation which just needs to be selected by knocking out the‎ remainder. Also, you have noted that horizontal transfer, even between unrelated bacterial species, begins almost immediately, when they are mixed  together. Given this, it seems to me that antibiotic resistance has taken a surprising long time to spread and become a major health concern. It could be, that the metals in our environment were holding it back, until recently, when our metal pipes and handrails were replaced with plastic and plastic coatings, and we reduced our use of coins in favour of plastic cards, paper, and electronic transactions.

The second remark--about mosquito's stance on it's legs--left me puzzled as to why it wasn't understood by the team. Having spent many a night scanning my walls and ceilings for nearly invisible mozzies, that whine in one's ear, as soon as the light is turned off, and then vanish again when it's turned back on, I had become very familiar with the, two back legs in the air‎, stance of the common mosquitoes, here.

I had assumed this was a general thing among those that hold themselves at an angle to the surface, but, following your team's confusion, I checked more Google images, and see that there are, indeed, as many pictures where all six legs are used, as there are of those where the back legs are held aloft or just left loose. I don't know how many species I'm looking at though.

One could imagine that the back legs might be needed for purchase while the proboscis was penetrating the skin, but then can be relaxed as‎ grip is transferred to the proboscis itself; but those on my walls hold their back legs aloft though they are not feeding, so it seems to be a preference, or have a specific purpose.   I had speculated that the raised legs may serve as aids to sensing air currents, and so contribute to the mozzie's uncanny ability to avoid swatting hands! Possibly the stripy legs of some species could be used in signalling too.

Anyhow, I have always found this stance an interesting observation. I further note, that the same places where the mozzies land, are frequented by Pholcus 'daddy long legs' spiders, but they rarely get caught. Both the spider and the mozzie have the same habit of doing high speed push-ups on their spindly legs, from time to time. I hope it's not catching!  :)

Hope this explains my points a bit better.
Many thanks for your, always thought provoking, podcasts.

(Weather now uniformly grey, cool, and still.)

Vincent: I asked Kristen Bernard at UW-Madison:

Mosquitoes often don't use the last pair of legs, but will use all six for balance especially once blood fed.


Friday, 23 September 2016 00:25

TWiM 135 Letters

Written by

Reed writes:

Dear Vincent, Elio, Michael, and Michelle,

I've just recently finished TWiM number 133 and wanted to comment about the use of the term "secondary metabolite" throughout the episode and often in the primary literature. Michael pointed out that a secondary metabolite is a molecule that is produced by an organism as it reaches stationary phase.

This is actually one of several characteristics that are used to define what a secondary metabolite is. Other common features are that secondary metabolites are "small" molecular weight compounds, they are not involved in the normal growth of an organism, and that they are dispensable for growth and fitness of the producing organism.

However, while many of these molecules are non-essential under laboratory conditions, they may be critical for survival under natural conditions. For example, siderophores are critical for scavenging iron under iron-replete conditions. Pyocyanins produced by Pseudomonas aeruginosa are involved in redox homeostasis. Bacillaene produced by Bacillus subtilis is essential for defense against lysis caused by Streptomyces sp. Mg1 and predation by Myxococcus xanthus. Lugdunin highlighted in the episode is another such case.

Additionally, many of these molecules are produced during multiple growth phases and are not exclusively limited to stationary phase. Taken together, these few examples illustrate that secondary metabolites may be far from "secondary" in their physiological importance. It is for these reasons and more that many have taken to calling these wonderful molecules "specialized metabolites"!

Thank you for the podcast!

Anthony writes:

He withered away for 7 years. Doctors didn’t realize his passion was killing him.
According to the paper, when doctors initially tried diagnosing the man’s illness, they overlooked his daily hobby: playing the bagpipes.
Tests conducted on the man’s bagpipes found a slew of fungi and yeast living inside the musical instrument.
Inside the air bag was a mixture of Paecilomyces variotti, Fusarium oxysporum, Rhodotorula mucilaginosa,and Penicillium species. In a petri dish, they formed a psychedelic swirl of green, orange and red mold.
Henrik writes:


thanks for providing so much information!

I have a mast cell activation syndrome and recently was by Prof. Dr De Meirleir in Brussel to look for chronic infections as a possible cause for mast cell dysfunction. He found that I have positive serology for Tularemia, so it seems that I was in contact with the any of the F. organisms.

He did some follow up tests I will only get to know next month.

My question is: Can the organism F.T. establish chronic infections or will the host either always die or kill the pathogen completely?

Thank you very much,


I asked Katy Bosio:

There have been a few reports of chronic infections with Tularemia, but I think those were largely restricted to the early days of antibiotic therapy (see Public Health Reports, 1926, 41:1341) and were symptomatic.  They also started with a known exposure to F. tularensis.

It sounds as though the listener may be asking if F. tularensis can cause sub-clinical disease, i.e. infection without detected signs of illness.  There is not much data on this either, but there have been some reports suggesting that it is possible (Emerging Infectious Diseases, 2010, 16(2); Emerging Infectious Diseases, 2015, 21(12)).  


Catharine (Katy) M. Bosio, PhD
Senior Investigator
Immunity to Pulmonary Pathogens Section
Laboratory of Bacteriology
Rocky Mountain Laboratories
Hamilton, MT


Wednesday, 07 September 2016 23:53

TWiM 134 Letters

Written by

Nathan writes:
Dear Vincent, Elio, Michele & Michael,
Thank you all for the wonderful podcast!  It’s a great gift to humanity and science communication.  It would be great if you could discuss the really interesting paper by Din et al recently published in Nature.  TWiV listeners know about viral-based anti-cancer therapies and successes such as Amgen’s T-Vec.  Now here’s a bacterial based approach.
Keep on podcasting.
Nathan in Chapel Hill

Cindy writes:

Hi TWiMmers,
I'm finally writing to say how much I enjoy your podcast after a year of listening. I was just listening to the latest episodes for a while because I'm lazy and you have years of podcasts to go through... but you weren't updating fast enough to satiate my appetite. I have been going through your feed for the last couple of weeks (while still listening to the latest updates) and cannot believe the goodies I've been missing out on! I considered #11 to be my favorite until I listened to #131 just today. I try to take anything about the microbiome with a grain of salt, as Elio suggests, but find myself picking my jaw off the ground after each episode that focuses on it. The way you TWiMers present the data and explain the experiments (either good or bad) make them easy to understand for us laymen/women. I knew nothing about bacteria other than there are really gross ones in bathrooms until this last year when I decided to go back to school for a marketing degree and fell in love the first time I looked through a microscope. I'm 27, a first year college student, mother of one, starting a career in Microbiology from scratch and still can listen to your podcast with some understanding because of how well you present it. Every episode I listen to keeps me hungry for more and so intensely curious about the world that is all around us and is so vitally important, as we continue to find out, that I sometimes finish an episode almost giddy with excitement over the work that is being done. Episode #131 is one of those episodes. Thanks for taking the time to spread the good word that is science and thanks for keeping it accessible.

Keep up the good work!

Steve writes:

Hi Microbies,

A research snippet mentioned in this week's Lancet, prompts me to get in touch with a couple of questions I've been meaning to run by the team:

Firstly: I've been wondering, while reading and hearing of all the remarkably technological work going into characterising the gut microbiota by brute force processing, why I never hear of 'gut gas fingerprinting', as a more simple method of characterising the makeup and activity/health of both the microbiota, and the host?

It seems to me, that a 'cheap and cheerful'‎ GCMS readout from a fresh faecal sample, could actually prove to be a very useful diagnostic and research tool--particularly so, if trace gas composition could be associated with particular microbial communities and disease conditions. Maybe microbiome researchers should routinely do GCMS on their samples when they do their PCR etc: it could reap great rewards as the data mounts up.

This actually struck me, when I was listening to Dickson discussing the 'foul smelling diarrhoea' associated with Giardiasis: most people probably think that all faeces smell foul, so how is the patient to describe degrees of foulness? This could be quite important to me, as I am disabled by severe bloating in combination with severe cramping in the small intestines, but, there seems to be no way on offer from doctors, to find out what is going on, other than occult blood tests and x-rays that show nothing.‎ Colon checks out OK, but what of the rest?

I've had breath tests that were indicative of overgrowth, but not of what by (This did not respond to penicillin antibiotics.).  At the same time 'normal' bowel movements can give off a powerful, almost petrochemical/mercaptan odour, which, most certainly is foul.   It seems to me, that routine GCMS‎ fingerprinting, could remove the uncertainties associated with describing odours, and be a valuable aid to diagnosis and identification of problems in hard to reach places.

The article that reminded me to ask about this, was actually on the issue as to whether, or how much, microbial gases 'control us'‎ by the production of 'gasotransmitters', so it looks as if gas and trace gas analysis could determine good biomarkers for all manner of purposes.  

Come to think of it, I do remember that someone was trying to develop an 'artificial nose' for detecting disease states in similar manner to the dogs that we hear of that can smell skin cancers. So gas/VOC sampling, both internal and external, surely should be getting at least as much attention from microbiologists as whole microbiome DNA, proteome, etc. sequencing?

What do you think?

Secondly: I've been listening to your various conversations on hand washing and ‎the problems attendant on trying to control spread of infections. I've been meaning to ask two things:

1: How the heck does anyone clean under fingernails, when most bathrooms do not seem to contain nail brushes, and the brushes available in shops become like the one in the attached picture, very quickly?  The only way I've ever really got my nails clean was with a high pressure flat jet on the garden hose--which is not really practical indoors. Perhaps there is scope for some kind of bathroom jet nail cleaner? Or an entire rethink of the bathroom basin to make it an enclosed device for jet-sterilising hands only.

2: For Michael:  As a child, I remember being, frequently, told to wash my hands after handling money (which in those days meant big coins), because 'you don't know where it's been'. Despite this, most kids would have a few big copper coins in their pockets, most of the time, and be continually handling them with sweaty fingers (Especially holding them still while running!).   

Children, and a good many parents, would have had copper, silver, and brass in appreciable concentrations in the sweat of their hands, almost all the time.‎ Far from being agents of disease spread, it seems likely that the universal use of copper and silver coinage must have played a big part in the prevention of disease spread.

(Actually, a lot of people don't even seem to like pockets these days, so that might be another confounding factor I hadn't considered. Perhaps the answer is to make mobile phone covers of copper: phones rarely leave most people's hands?)

In addition to this, there was pretty much universal use of copper and brass for door handles, hand rails, curtain rails, door push plates, pots and pans, keys and locks...   We were constantly charging ourselves up with microbe killers wherever we went, and this was obvious from the beautiful sheen/patina on 'public metal'‎ created by the touch and sweat of many thousands of hands.   How quickly those coins went dull and green when left at the back of drawers...   (How easy it is to recall the taste of copper! My mouth waters at the thought! I wonder if today's children know that taste?)

So, it seems quite plausible to me, that the switch to paper and plastic money and electronic transactions, and away from the best metal in the coinage that remains, coupled with the near disappearance of decent metal door and window 'furniture'‎, bathroom plumbing, and handrails, could be the single most contributive cause of the modern spread of diseases, by contact.

What does the team think?

Your very good health.


At a sticky 24C, as it's better than opening windows and letting mozzies in!  (Ooh: Which reminds me: Why do they have 6 legs when they only use 4?  :) )


Saturday, 20 August 2016 04:41

TWiM 133 Letters

Written by

Arthur writes:

Hello TWIMers!

I'm a graduate student working in mycoplasmology and I  must say I've been overjoyed to hear the past few episodes mention our tiny friends!

Elio's mention of their unique mechanism of moving ("Gliding Motility") made me think of a recent paper from the group in Japan under Dr. Miyata - you may find the paper quite interesting (attached)! They've done a lot of work on mycoplasma motility, and local US researchers such as Dr. Mitch Balish at Miami University also have made great advances in this field.

In discussion of the Mip/Mib system, one thing that has caused some head scratching in our lab has been why the microbe cleaves the Fab portion rather than the Fc? The human species (M. genitalium and M. pneumoniae) don't have the serine protease (at least based on homology searches) and bind to IgG nonspecifically - it makes you wonder why the microbe has conserved that binding protein? Quite a neat area that needs more work!

Thanks for such an interesting podcast and keeping me preoccupied during my hours in the mouse facility!

Warmest Regards,


Frank writes:

Dear Drs. of TWIM,

Two observations on pili conduction.

TWIM #51 featured Hazel Barton discussing her discoveries of microbial excavation of caves.  Barton’s comments on the role of Geobacter electron transport in speleogenesis would be very interesting.

Secondly bio-batteries would seem to be far ahead of their time.  These energy sources that are so valuable to low C/V biological systems are likely not going to be useful in our crude, relatively high C/V electronics.  I have to imagine that our current electronic technology will eventually discover and utilize biomolecular processes to accomplish computing and communication.  At that time, bio-batteries will come into critical use and we can start to approximate the complexity and elegance of multicellular organisms.

August Gloom pervades the northern California coast where the temperature is Ugh point 7 (15.5C) and the humidity is only a optical tease of much needed falling water.
Thanks for all the education.  Your importance can’t be overestimated!

Best Regards,

Aptos, CA


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