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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 137 Letters

Daniel writes:

Hello,
Long time listener, first time writer. It has been far too long for me to offer my sincere gratitude for the podcasts. Some years ago I was a welder working a very boring job and I managed to get through my day by listening to podcasts and lectures. These podcasts and lectures convinced me to give up my boring day job and go to the excitement of university. There I progressed in biochemistry and developed a love for science, and went on to a Masters and am now working on my pHD. You can’t imagine the excitement and fulfillment when I heard our paper was featured on your podcasts (That one about diderms and monoderms). All that work seems to have paid off and it truly feels like I am a real scientists now.

So thank you!

I feel I need to give a shout out to my pHD program. The pasteur institute has an international pHD program where they call for applicants every year and provide an amazing 3-year pHD program. This institute is probably one of the best for doing science and I couldn’t picture a better pHD. Here is a link:
http://www.pasteur.fr/en/teaching/doctoral-programs/pasteur-paris-university-international-doctoral-program

As for our paper thanks for the nice overview. To address Dr. Schaechter’s comments about seeing how the systems compare between E. coli and the Negativicutes I have this for you:

First of all remember E. coli is one of the most “evolved” bacteria there is. They have a large genome and incredibly complex systems (probably not the best model system due to that, but that’s history). See attached tree (It is pretty rough, so don’t make a big deal about the deep nodes, Monoderm phyla in grey, No root so don’t pay attention to what is ancient). The Negativicutes are so extremely distant that it is amazing they posses the same systems and any genomic synteny. However with the pili (some supplemental figures in the paper) it is clearly the same system. The BAM/TAM system is drastically different and matches the more closely related Fusobacteria, and other Terrabacteria beautifully. We have a lot more to say on this story and we will have more fun articles coming months :)

Cheers,
Daniel Poppleton

chart
Anthony writes:

http://www.pnas.org/content/113/34/E5062.abstract

Climate influence on Vibrio and associated human diseases during the past half-century in the coastal North Atlantic.

 

TWiM 136 Letters

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.

http://www.thelancet.com/journals/lancet/article/PIIS0140-6736(16)31420-9/fulltext?elsca1=etoc

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

All the best,

Steve
luton
England

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:

http://www.bbc.com/news/science-environment-37287715

"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.

https://static01.nyt.com/images/2016/06/01/health/well_mosquito/well_mosquito-facebookJumbo.jpg

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.

Steve.
(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.

 

TWiM 135 Letters

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.

https://www.washingtonpost.com/news/morning-mix/wp/2016/08/23/he-withered-away-for-7-years-doctors-didnt-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:

Hello,

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,

Henrik

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)).  

Best,
Katy

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

 

TWiM 134 Letters

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?

http://www.ncbi.nlm.nih.gov/pubmed/27389418


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.

Steve
Luton
Bedfordshire
England

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?  :) )

 

TWiM 133 Letters

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,

Arthur

https://www.ncbi.nlm.nih.gov/pubmed/27073090

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,

Frank
Aptos, CA

 

TWiM 132 Letters

William writes:

Hi TWiMers;

It is a nice late July evening here in Berkeley - 60F/15.5C - no fog, but we have had a bit less than usual summer fog this year.

Ran across this article which is fascinating  because it falls into the category of "what you thought was obvious, in fact is not."

"Lichen: Apparently Happy Couple Really A Threesome"
.......
"Lichens come in two basic flavors. One forms a thin, film-like layer on rocks and trees. The other kind is composed of "macrolichens" that grow big leafy, branching or vine-like structures. It's the latter that seem to harbor the yeast.
The discovery started when Toby Spribille, a postdoctoral fellow in McCutcheon's lab, was studying two lichen species collected from the mountains around the Missoula, Montana campus - Bryoria fremontii and B. tortuosa. The two species are distinguished by the presence of vulpinic acid in B. tortuosa, which also gives it a yellow colour. However, genetic tests showed that the known fungus and alga in both lichen species were identical.
But Spribille and McCutcheon found the genetic signature of a third species - a basidiomycete yeast, present in both of the lichen species but more abundant in the yellow version. They and their colleagues went on to test 56 different lichens from around the world, and found each had its own distinct variety of basidiomycete yeast."
See "Lichen: Apparently Happy Couple Really A Threesome"http://www.science20.com/news_articles/lichen_apparently_happy_couple_really_a_threesome-177105
Bill (William) Johnston
Berkeley, CA

Anthony writes:

https://www.theguardian.com/science/blog/2016/jul/27/lets-celebrate-150-years-of-beatrix-potter-author-scientist-and-fungus-lover

:...
Until quite recently, Potter’s accomplishments and her experiments in natural science went unrecognised. Upon her death in 1943, Potter left hundreds of her mycological drawings and paintings to the Armitt Museum and Library in Ambleside, where she and her husband had been active members. Today, they are valued not only for their beauty and precision, but also for the assistance they provide modern mycologists in identifying a variety of fungi.
In 1997, the Linnean Society issued a posthumous apology to Potter, noting the sexism displayed in the handling of her research and its policy toward the contributions of women.

Christoph writes:

Dear TWiM overlords (in a gender neutral way)!

Michael had a very interesting interpretation of what coccolithophores were, when commenting on Kyle's letter in TWiM 131!

He correctly identified two out of the three Greek/Latin words in there, but that steered him in a in funny direction, as he thought they were rock eating cocci and not Haptophyte algae.

Let's see what I can remember from learning two dead languages in "Gymnasium" (German grammar school):

Cocco-litho-phore consits of "cocco-" from Greek kokkos = berry (score Michael) , "-litho-" from Greek lithos = rock (score Michael) and "-phore" from Latin ferre = to bear / to carry (this one Michael got confused with trophos = feed)

So Michael turned the "Cocci-Rock-Bearers" into "Cocci-Rock-Eaters". Close, but no cigar!

Indeed the, the "Cocci-Rock-Bearers" got their name from carrying tiny scales of calcium-carbonate, the coccoliths (I presume this was close enough to be called "rock" since their fossilised remains makes those impressive cliffs of Dover in the UK). Their ability to turn carbon dioxide into calcium carbonate combined with their high abundance in temperate oceans makes them highly important to the global carbon cycle, but unfortunately also highly susceptible to ocean acidification. One of their prettiest members Emiliania huxleyi has even been featured on TWiM before (TWIM 34 https://en.wikipedia.org/wiki/Emiliania_huxleyi).

Hope I didn't screw this up too badly and embarrass my former Latin/Greek teachers...

Keep up the great work, the TWiX empire is awesome!

Maybe you could feature more free living eukaryotic microbes (and their viruses)?! It seems like they get lost somewhere in the gap between TWiM and TWiP, but their rare appearance is always a delightful listen (like TWiM 94)!

Chris

PS: The weather in Vancouver BC is currently 21˚C, 73% humidity, 0% chance of precipitation and apparently pretty windy with 29km/h (although a quick look out the window can't confirm this..)

 

TWiM 129 Letters

Steven writes:

Dear Vincent et al,

Firstly, congratulations for keeping up such a wide range of thought provoking podcasts, and maintaining such a tremendous output. I find they all leave me with more questions than answers, which is, I think, a sign of good science.

On the latest TWiM, I listened with fascination to Elio's round up of species able to manage without mitochondria (I wonder: will Wolbachia ever be reduced to the status of organelle?), but then I found myself feeling decidedly uneasy as I listened to the review of the paper on using a phage lysate as a novel antibiotic against bacteria.

Our 'traditional' approach to antibiotics (and, indeed, anti-cancer drugs, and pesticides), through simply prospecting for active chemicals in the environment‎, and then using them in a haphazard way--both through the profit motive, and misuse--has, in every case, led to the development of resistance and the danger of a return of morbidity to pathogens long thought 'tamed'.

Isn't it time we learnt our lesson?   This new attack on the natural resource offered by phage, clearly shows that we have not. By all means, search for an active phage, but, for all our sakes: don't go spiking its guns!

I found myself with a sense of deja vu as I recall my concerns when B.t. products began to be used as pesticides, even though the live bacteria had long been used as a proper biological control--no patent fortunes to be made in that, of course.   

Using the natural process, bacteria multiply in the target species and destroy it from within: using bacterial products as sprays that don't multiply, the pest may or may not absorb a lethal dose, and resistance is much more likely to develop (Applying it via the GM route, pests are still able to sample a leaf, and reject it and go somewhere else: not so if they had swallowed whole bacteria.).‎

No doubt, resistance develops more slowly in insects than with the case of antibiotics and bacteria, but I think that the end result is inevitable: a useful living biocontrol has been rendered ineffective, due to our obsession with finding the active ingredients of everything and using them 'pure'.  (The same thinking was applied to the food industry when 'nutrition' kicked off in the 19C and gave us white bread and sugar, from which we still have not recovered.)

Whilst prospecting for antibiotics has been recently given a second chance through the new methods of cultivating bacteria‎ 'in the wild', it seems clear that there is every intention of going on with 'business as usual', mass producing every new find, and then cashing in until resistance develops.

Meanwhile, other countries have, apparently, been using the much more logical approach, of letting whole phage target, and destroy, pathogenic bacteria, all along.   Why are the 'Westernised' countries not pursuing what would seem to be a much more likely way to  combat bacterial drug resistance than carrying on the way we have been?  [Presumably the drug cos don't see fortunes in that approach.]

The rather lame 'excuse' seems to be that us fussy 'Westernised' people would not accept 'live' viruses inside us, whereas we don't mind poisonous chemical drugs. I think that the willingness with which we shovel 'probiotic' yogurts, and even consider stool transplants, demonstrates that it would not be so difficult to market phage as the next big natural medicine--And in this case, it really would be medicine!

Undoubtedly, phage therapies will have their own intrinsic problems to overcome--getting around our immune defenses for one--, but the fact of their quite long history of use shows that ways have been found.   So: What right do we, who have squandered all our 'magic bullets', have to start stripping down the medicinal phages used by other nations, to their basic components, in order to extract and squander the magic from them too?  

What we witness in the phage lysate paper discussed on TWiM, is the start of an assault on the essential medicinal resources of other nations, that could saddle them with pathogenic bacteria made immune to their natural phages, and, leave them and ourselves powerless to fight disease.   And, in a worst case scenario, we might even upset the entire balance between phage and bacteria that has kept the latter under control for billions of years.

I am, of course, only a lay observer of all this, but it rather strikes me, that playing loose and free with the essential tools and weapons with which phages prevent our world from simply piling up with bacteria, when we know that our own methods always result in resistance‎, is a much more dodgy thing to contemplate, than all those 'gain of function' experiments we argue about.   These, indeed, could be called 'loss of function' experiments, because, used the way we know they will be used, they, indirectly, could result in the reduction in effectiveness of some of the most vital housekeeping components of our ecosphere.

I hope I'm wrong, but I think history is on my side.

Sincerely,

Steve
Bedfordshire
England.

Ben writes:

Dear Twimers,

I recently discovered your excellent podcast and have been going back through your archives discovering many gems. My favorites so far include the discussion about the Bobtail Squid with Margaret McFall Ngai in TWiM #10, the discussions of Ehux in TWiMs #34 and #37 and the discussion of Centenulid Flatworms in TWiM #21.

I'm an artist and have no scientific training so I listen without expecting to understand everything, but when things get a little too technical I'm always sure that you all will bring the discussion back around to a point that I can readily understand. This is something I really appreciate so thank you for your effects to clearly communicate the intricacies of the fascinating and exciting world of microbial science.

I recently came across this paper that I thought might be of interest

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0144270

This is an example of a substance that is generating what seems to be a beneficial alteration of the gut microbiota. I found it particularly interesting that the species involved is Akkermansia muciniphila-one that regulates mucus in the gastrointestinal tract. Given that the mucosal lining of the intestine is an important area for communication between host and microbe I wondered whether the ecology of the intestinal mucosa might be in interesting subject for a future TWiM.

Kind Regards

Ben

Sydney, Australia

Anthony writes:

Experimental evidence of a symbiosis between red-cockaded woodpeckers and fungi

http://rspb.royalsocietypublishing.org/content/283/1827/20160106

 

TWiM 128 Letters

John writes:

Dear TWIM Team,

First of all, thanks for the supremely informative and entertaining podcast. As a biologist who stumbled into my passion for microbiology almost by accident (as a student, I began my research as a herpetologist and was converted while working with the cutaneous microbial assemblages of woodland salamanders), your podcast serves as a primer for many topics that would otherwise require hours of comparatively boring research.

One trend that I hear often repeated is that every microbiology student can't hope to be a PI in an academic lab, which is very true. I currently work in the R&D department of a small biocatalyst company, and wonder if more attention shouldn't be paid to careers for microbiologists in the private sector. While R&D doesn't afford one the same sort of research freedom that academia can boast (I have had to leave numerous interesting but commercially irrelevant questions relegated to the margins of my notebook), it does give you the opportunity to research a variety of interesting aspects of applied microbiology.

There are a few research conferences coming up this year, namely the Society for Industrial Microbiology and Biotechnology (SIMB) annual meeting (http://www.simbhq.org/) and their more specific Recent Advances in Microbial Control (RAMC) symposium (http://simbhq.org/ramc/). Perhaps the list of topics might provide the basis for a TWIM exploring some of the applications of microbiology in agronomy, animal husbandry, bioremediation, wastewater treatment, and other areas. Academic and clinical microbiology seem to get all the attention, and perhaps deservedly so, but there are other options out there for a microbiologist open to branching out.

Thanks again for the fantastic podcast, keep up the great work.

Best Regards,

John

Ross writes:

Hey TWiMers. I very much enjoyed your discussion of the content of pro-biotics a couple weeks ago. It was interesting to me as previous research I have seen indicated many of those probiotics had little effect on the microbiome, or even had very few live bacteria reaching the gut. Certainly the consensus seems to be they are not very helpful as a health product. But the fact many of those products contain what they claim for the most part was enlightening. This latest research out of Copenhagen may be of interest to you, it seems to further cement the idea that these products are essentially worthless as health supplements. I wonder how this compares to the TWiMers assessment of the current literature? https://www.theguardian.com/science/2016/may/10/probiotic-goods-a-waste-of-money-for-healthy-adults-research-suggests
 
P.S I applied to be a communication ambassador this year for the Australian Society of Microbiology and am very excited to have been successful. I would love TWiM listeners to follow me @rossbalch and the society @aussocmic and keep up with my adventures in my PhD in respiratory virology as well as sharing and talking about the latest in microbial science throughout the year.
 
Regards, Ross Balch
BAppSc(MedSc), BAppSc(Microbiol), BBiomedSc(Hons)
 
School of Biomedical Sciences
Queensland Institute of Technology
Centre for Children’s Health Research (CCHR)
Institute of Health and Biomedical Innovation (IHBI)

Hunter writes:

Greetings!
 
I came across this article today and had to share it. I wasn't sure which show to send it to, as the microbe described is related to Giardia and Trichomonas, but I figured TWiM was still more appropriate than TWiP.
 
Surprise! This eukaryote completely lacks mitochondria:
http://phys.org/news/2016-05-eukaryote-lacks-mitochondria.html
 
The article mentions that they're using sulfur with a system acquired from bacteria to replace the mitochondria, and that the researches want to try to find when the mitochondria were lost. However, I didn't see anything mentioning evidence that mitochondria were ever there.
 
Is there some evidence that the microbes used to have mitochondria but lost them, or is it just assumed that they must have had them at some point and lost them?

It seems to me that it would be possible that some microbes could have evolved similar traits to other eukaryotes without having taken up mitochondria.
 
I also was thinking about the possibility that two organisms could evolve to have similar looking genomes completely independently of each other simply because similar pressures in different places could cause similar genetic patterns to emerge. The result being two organisms with one or more major differences that appear far more closely related than they really are.
 
With ongoing increases in information that we can gather about organisms, it seems like our current system for categorizing life is becoming less and less able to accurately represent the way different organisms are connected. When I was in school (not too long ago) we were taught to remember the hierarchy of life using: Kings Play Cards On Fat Green Stools, but this system only goes down to the species level, which seems to leave out at least one level of categorization out.
 
If the finding that this eukaryote doesn't have mitochondria, which seems like a pretty major difference to others, I would expect to see a new tier added between the currently existing top level eukaryote category and all the current sub-categories that splits the mitochondria and non-mitochondria having eukaryotes, with the currently existing eukaryotes mainly existing under the new mitochondria having category.
 
With current technology, it seems like it would be more efficient to focus on cataloging organisms and their traits and thinking of them as a relational database where you look for things based on one or more traits with less focus on trying to specifically build a family tree like hierarchy that can be more difficult to adjust to fit new information. For example, with a trait based model, a new finding like this would simply become a new attribute on any appropriate organisms. This, in turn, would cause said organisms to be listed if you were querying all organisms that were both eukaryotic AND lacking in mitochondria without needing to change the categories, or make changes to any other organisms.
 
With that kind of data, it seems like constructing a hierarchy could be done programmatically, at regular intervals (annually, for example) and with all the needed changes to make sure all life on the tree is at an appropriate level (and that there are enough levels).
 
Anyway, I don't know if most of this sounds like the rambling of someone that clearly doesn't have a background in biology, but I figured I'd share some of the thoughts I had after reading the article.
 
Hope all is well back East. It's currently 24C and partly cloudy here in Irvine, CA with a 51% chance of rain that I'm sure we won't see.
 
PS: For the hardcore condition fans:
It feels like 24
Wind is out of the SW at 14km/h
Visibility is 16.1km (not counting the fact that between walls and other buildings I probably can't see more than 100 meters.
 
____________________
Hunter Curren
QA Analyst 3 : Hearthstone
Blizzard Entertainment

William writes:

An interesting anomaly that you might be interested in discussing:  A eukaryote without a mitochondrial organelle
A. Karnkowska, et al. A eukaryote without a mitochondrial organelle. Current Biology. Vol. 26, May 23, 2016. doi: 10.1016/j.cub.2016.03.053.

 

TWiM 127 Letters

Stefan writes:

Just discovered this nice episode.
Well made and nicely discussed comment on our pack-hunting paper; quick reply to the question what would happen if you add one single amoebae: it would multiply and a clonal pack would do the same thing as observed (they were actually grown from clonal cultures).
But let's say if only one amoeba was existing before trapping the nematode- no idea if that would be able to kill it alone - would be a nice side study!
very interesting hypotheses you came up with, we should study some of it
Keep on with this great work!
Stefan

Anthony writes:

Branchial nitrogen cycle symbionts can remove ammonia in fish gills

Just looking at the abstract, I wonder if the relationship really is commensal.  Without the bacteria in the gills, won't the ammonia still be carried away from the fish?
# # #
Branchial nitrogen cycle symbionts can remove ammonia in fish gills
http://onlinelibrary.wiley.com/doi/10.1111/1758-2229.12407/full

Abstract
Knowledge of the mechanisms by which fish excrete their metabolic nitrogenous waste and insights into nitrogen cycling in aquaculture systems is of utmost importance to improve the sustainable commercial production of fish. In fish, most nitrogenous waste is excreted via the gills as ammonia, a potentially toxic nitrogenous compound. In this study; activity assays, physiological experiments, molecular analysis and microscopy were used to show that the gills of fish harbor a unique combination of hitherto overlooked nitrogen-cycle microorganisms that can theoretically detoxify excreted ammonia by converting it into inert dinitrogen gas. By doing so, these microorganisms may benefit from the ammonia supply by the host and prevent the build-up of this compound to toxic concentrations. This novel relationship between vertebrates and microorganisms may shed new light on nitrogen handling by ammonotelic fish species. This article is protected by copyright. All rights reserved.

And

Copper pajamas?

http://www.mrsaidblog.com/2016/03/04/copper-pajamas-an-18-year-old-school-girl-beats-scientists-to-a-mrsa-remedy/

"...
So by the time Gemma was in the hospital fighting for her life, Amber was ready. She brought in copper pajamas, bedding, socks, and a hospital gown for Gemma. (Since copper is a metal the fabrics were a blend of 60% copper, 20% cotton, and 20% bamboo.) Gemma was skeptical at first but within a couple days she felt much better and noticed the open wound was decreasing in size. “It was incredible,” said Gemma, “the nurses took swabs from my stomach daily and they always came back infected with MRSA, but a few days after wearing the copper-infused clothing, they came back negative. You wouldn’t think something so simple could make such a huge difference but I could feel the difference in my skin almost overnight. Instead of feeling lethargic I felt brighter, more alert and healthier. More importantly, I was healing. It was a miracle.”

Clinical trial mentioned in response…
http://www.sciencedirect.com/science/article/pii/S1201971214000599


Suzanne writes:

You're right, I do hear women saying "guys" plural to others in a group of women. But I still argue that if I said "That guy over there." you'd be more likely to expect to turn and see a man than a woman. So it isn't really neutral.

I vote for the spread of y'all!

PS. I catch myself at it, too. I will also try to be more vigilant!

Pat Schloss writes:

Hey gals,

Although I’ll never be accused of being part of the language police, I was taken aback by Vincent and Michael’s reaction to Michele’s comment on TWiM #125 regarding the use of “guys” when referring to people that are involved in computer programming. As you may know, it is thought that there are many small biases throughout the career development of female scientists that discourage them from pursuing specific disciplines - particularly computer science. So it would be worth reconsidering the collective nouns we use to refer to people within science.

To bring some data to the conversation, here’s a large, but admittedly non-scientific survey of 2300 individuals (http://jvns.ca/blog/2013/12/27/guys-guys-guys/).  The survey showed that men are more likely to think that “guys” is gender neutral when referring to people within a computer science context. Regardless, I think we owe it to our female colleagues and trainees to use the terms that are the most inclusive.

As someone that runs a lab with a heavy bioinformatics focus, it is very important to me to maintain a strong balance between men and women knowing that this is difficult given the poor representation of women in computer science. Both programmers that have worked for me have, in fact, been women. To call them “guys” would be obviously wrong. All kidding aside, I would be unlikely to call them “gals” as well. Instead, I have been working cut “guys” out of my language and go back to my Missouri roots by instead saying “y’all”. If nothing else, every time I force myself to use this odd slang, I remind myself to check my unconscious biases and to be better.

Happy Sciencing!
Pat Schloss

 

TWiM 126 Letters

 

Anthony writes:
An Abandoned Sailor’s Infirmary in NYC Where Cholera Bacteria Was Discovered
http://untappedcities.com/2016/03/10/an-abandoned-sailors-infirmary-in-nyc-where-cholera-bacteria-was-discovered/

Neva writes:

Hello clever TWIM ers,
A rather urgent detective story that TWIM might be interested in talking about. People in the area must be very spooked.
Neva in Buda
Deadly disease outbreak in Wisconsin baffles public health officials
A common and usually harmless microbe is causing a mysterious cluster of deadly bloodstream infections in Wisconsin.
http://www.statnews.com/2016/03/14/disease-outbreak-wisconsin/

Dennis writes:

Hi Docs, this cnn article gives some info on a continuing Elizabethkibgiam outbreak.
Rarely seen blood infection outbreak continues; source remains mystery
CNN
The rarely seen blood infection Elizabethkingia has been found in a Michigan resident. It has sickened dozens in Wisconsin since November. Read the full story


Best,

Dennis

vr: see http://www.promedmail.org/post/4158063

Elizabeth King (used to be Flavobacterium)

Suzanne writes:

Guys isn't gender neutral it's gender absorptive. It's used the same way it became standard over the last few hundred years to use he as a general third person singular pronoun (before that they was acceptable). Just because some women are OK with it doesn't mean the rest of us can't be annoyed by it. If your students will call a specific, individual woman a guy then I guess I'm wrong and it's honestly becoming gender neutral. But I never hear anyone doing that.

 

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