TWiM 74 Letters

Katja writes:

Thank you for the great podcast! You've explained our story very well and it was funny to listen to it. I didn't know that "Speak friend and enter" is from lord of the rings! I just wanted to explain the name CYCLOPS because this was a question mark in the podcast. This is a link to Yano et al. 2008 where they describe the cyclops mutant phenotype in fig. 1. In the WT the fluorescently labeled rhizobia enter the root by the formation of an infection thread. In the cyclops mutant, the root hair curls around the bacteria but further infection is impaired. And because this looks like an eye of an cyclops, the mutant derived its name from :-)

Laurel writes:

Hello all! I am a graduate student at UNC Chapel Hill in the Microbiology & Immunolgy department, and since my lab is mainly focused on the immunology section of that I try to supplement my microbial knowledge with information gleaned from other sources like your podcasts (Though I am a particular fan of parasites and TWiP). And as you can probably tell from this comment being so behind, I am never caught up with the podcasts, though I listen to them regardless.

You all mentioned that perhaps due to the high salt levels and temperature of the lake the haloarchaea from TWiM 68 act very similarly to when you perform a transformation in their extremely high gene transfer rate. Wouldn't it be fairly easy to test this theory since the authors demonstrated that they grow at many different temperatures? You could follow growth at room temperature and examine if comparable gene transfer takes place. I just wondered if any had considered looking into that to determine if that is the case. Thanks!


Geoffrey writes:


While your show has been a real eye-opener for me in so many ways, much of my interest in the microbial world remains in the areas of endo- and ectophytic microbes, soil microbial ecology, and food / energy / raw materials fermentation. You speak frequently (and, I have noticed, rather lovingly) of exploratory deep genome sequencing just to try to find out what’s in the environment. Though a little more narrowly focused, that is exactly the kind of research that I am reading about frequently in my areas of interest. What is the microbiome of a Withania leaf?, miso?, apong (wine / beer from moldy rice)?, hydrogen-bubbling mud?, and other topics of that nature.

I won’t pretend to understand all the techniques that are being used to genetically identify the microbes in these environments but it is of interest to note that much of what we thought we knew due to culture techniques isn’t particularly accurate. Culture techniques often skew results towards easily culturable microbes which can greatly distort our reconstruction of microbial communities (especially reconstructions of microbial succession) and completely misses the contributions of NCO’s (Non-Culturable Organisms). Recent techniques involving direct analysis of DNA present has greatly expanded out knowledge of these communities but different techniques often produce different results. We are still expanding and improving these techniques and, more importantly, learning how to apply them so that they complement each other’s strength and weaknesses and give us unprecedentedly clear views of microbial communities.

With all that introduction done, I now present my question. I assume that deep genomic diving involves many of the same techniques used in the shallower explorations mentioned above and viruses definitely provide a deep and wide pool of NCO’s. Would you be able to discuss some of the major DNA / RNA detection techniques used in this field in terms of their strengths and weaknesses and how different researchers are overlapping their use to build robustness into their studies of microbiome and virome?

Thanks for the great podcast,


Alice writes:

First, thanks to Vincent et al for the wonderful podcast series (all 3). I am a fellow in pediatric infectious diseases (a fellow is the MD-equivalent of a post-doc for subspecialty training). Your podcasts are thought provoking and timely and always intellectually stimulating - so thank you.

In return, the temperature here in Cleveland Heights is currently 15oF, winds west at 7mph, humidity 72% and I'm really tired of winter.

Regarding TWiM #72: your discussion of this paper coincided with my caring for a patient with a surgical procedure known as a ureterosigmoidostomy, in which the ureters are implanted into the distal colon when the bladder is not present or can't be used for some reason (e.g. congenital malformation). In the process of caring for this person, I learned that there is a significantly increased risk of cancer developing in the bowel (see references below). After this surgery, the urine drains into the bowel and greatly changes the chemistry and flora present. Examination of the microbiota and/or metabolome of these patients may turn out to be quite interesting.

Thanks for making me think differently about our relationship to micro-organisms every day.

Alice Sato, MD PhD

1. Eur Urol. 2011 Nov;60(5):1081-6. doi: 10.1016/j.eururo.2011.07.006. Epub 2011 Jul

Tumor growth in urinary diversion: a multicenter analysis.

Kälble T, Hofmann I, Riedmiller H, Vergho D.

2. BJU Int. 2010 Mar;105(6):860-3. doi: 10.1111/j.1464-410X.2009.08811.x. Epub 2009
Aug 13.

Long-term outcome of ureterosigmoidostomy: an analysis of patients with >10 years
of follow-up.

Tollefson MK, Elliott DS, Zincke H, Frank I.

3. Acta Chir Belg. 2009 Jul-Aug;109(4):531-3.

Complications associated with ureterosigmoidostomy--colon carcinoma and ascendens
infection resulting in nephrectomy: a case report.

Turedi S, Incealtin O, Hos G.

4. J Urol. 1990 Sep;144(3):607-10.

Current status of tumor of the bowel following ureterosigmoidostomy: a review.

Husmann DA, Spence HM.

Clark writes:

I was wondering if you all had seen this recent paper on detection of oral bacterial DNA in synovial fluid. Given that one of the frequent hosts teaches dentists I would be especially interested in his comments about the relationship of periodontal bacteria in other diseases. I think it’d make a very interesting discussion for non-microbiologists like myself. (My background is physics)

A doctor friend of mine created an rss feed on the topic so it seems like there’s been a lot of work done on this.




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