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TWiM 65 Letters

Alexandra writes:

Dear TWIM-ers,

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

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

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

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

Thanks so much for reading!

Your faithful listener,

Alexandra

Peter writes:

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

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

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

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

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

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

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

Andres writes:

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

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

Keep up the great work!

Thank you,
Andy
Fremont, CA

John writes:

Dear TWIMmers,

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

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

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

--John

David writes:

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

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

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


Christyne writes:

Dear Vincent and fellow TWiMmers,

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

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

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

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

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

p.s. I love Elio's voice

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

Joe writes:

Dear TWiM folk,

Hi from Denver and ICAAC.

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

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

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

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

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

Best,

Joe

 

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