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TWiM 62 Letters

Robert writes:
In TWIM #60 @1:06:23 Michael Schmidt suggests that glucose for fermentation from biomass is a necessary step in production of fuel ethanol. Fuel ethanol and other low molecular weight compounds can also be produced by autotrophic anaerobic fermentation of syngas. Syngas is a mixture of carbon monoxide, carbon dioxide, and hydrogen produced by pyroclastic treatment of a wide variety of organic material including ligno-cellulose, recycled tires, sewage sludge, and natural gas or methane. These reactions have been studied for many years and are being commercialized by Coskata. www.coskata.com.
Never underestimate the ability of microbes to scrounge a living from nearly any environment with water and energy available.

Tim writes:

I am a Canadian, here in the USA attending graduate school. Occasionally I hear hints in Michael Schmidt's language that he might be a fellow Canuck (words like "university" and "zed", and of course his impeccable class and intelligence). Michael, thinking back I'm not sure you've revealed anything about your past prior to your days in Indiana (at least not in the TWiMs I've listened to - I'm still working through them). If this is on purpose I respect that decision (I don't mean to pry into personal lives) - I was just curious.

Happy TWiMing!

- Tim

Juan writes:

Hi, i'm currently a Bioinformatics and Genomics Phd student at Penn State with a masters in Computer science and statistics. I'm currently working in antibiotic resistance in bacteria. I'm almost up to par with twim and i'm very grateful for your insightful discussions and the time you put in teaching everyone. This has been a great foundation for my microbiological knowledge. Keep up the good work.

I recently had the good luck to meet Dr Jo Handelsman during a distinguished talk here in my department.

I'm also a listener of twiv and twip, but not as often as twim.

Anonymous writes:

Last year, I started teaching microbiology for students interested in health-related fields. I caught up on all past TWiM episodes to help prepare me for teaching. I have learned so much from the podcasts, and so much what I already knew has been reinforced! In particular, the recent mention of conjugation experiments brought back happy memories, since I worked on a self-mobilizing pathogenicity plasmid for years. Listening to TWiM has an added benefit, since my students think I'm much smarter than I really am. :-)
I'm from another country and a few days ago, I was talking to a colleague (also from another country), and we discussed our shock when we first came to the US and found that everyone who works in health care can simply go home in their work clothes. In fact, they almost seem to wear their scrubs as a badge of honor (Do you see my scrubs? I do really, really important work!). It is my impression that many cases of nosocomial infections are associated with health care staff (consider that renovating an entire building wasn't enough to get rid of Klebsiella, which was probably brought back in on the first day of re-opening by the staff). The staff carry these bacteria, fungi, and viruses in their noses, on their skin, hands, and clothes around with them. They leave work, stop to buy groceries on their way home, pick kids up from daycare/school, and take their clothes home and wash them with the rest of their household laundry.....
In a number of other countries, health care personnel have to change in designated rooms at the facility. Their uniforms have their names sewn in, or embroidered on, stay behind at the end of the day, and are properly washed by the facility itself. Personnel can (and sometimes are required to) showers before they change into their regular clothes and leave the facility.
Maybe I'm missing some crucial piece of the puzzle, but it seems like a relatively inexpensive and effective way to limit spread of antibiotic resistant bacteria to the general community. It may also have a positive outcome on the spread within the health care setting. I would appreciate it, if anyone on the podcast could comment on this.

Tim writes:

Hello TWiMsters! (I apologize if you receive this message twice, I just noticed that you have a contact form for sending emails.) I recently discovered the trifecta that is the TWi series, and now I can’t get enough of your discussions of all things micro. For graduate students like myself, keeping up with the scientific literature can all too easily become just a means for cramming information into our brains that we feel we “should” know. Not only do your shows keep my mind stimulated and expose me to scientific papers that I might not otherwise read, but the informal and enthusiastic nature of the programs are just the slap in the face I need to crawl out from under the stack of papers, and remind me that I actually love to learn about science and to think about the various implications that a particular finding or result might have. After listening to your conversational discussion format and your fantastic insights that tie together the biology of the organism (or virus – are viruses organisms?) with the environment, host, experimental techniques etc., I am finding new clarity in the way that I think about scientific problems and evaluate scientific papers. I can’t commend you enough for what you do. Formal presentations of scientific findings are a dime a dozen - listening to world-class scientists “chat” amongst themselves about current topics in microbiology is an invaluable resource that few people really ever get a chance to do, until now. THANK YOU!

On a scientific note, I was recently listening to TWIM #43 and your discussion on the stable formation of caveolae in in E. coli. It was mentioned that it had previously been thought that stable caveolae formation in eukaryotic cells requires cholesterol, to which Michael replied that “there is [no cholesterol] in our friends the bacteria”. Although this was and is true in the context of E. coli and the paper’s findings, I think it is worth pointing out that there are several described examples of free cholesterol and cholesterol-containing glycolipids in bacterial outer membranes – namely in Helicobacter, Mycoplasma, Ehrlichia, Anaplasma, Brachyspira, and Borrelia species. In Borrelia burgdorferi, cholesterol containing compounds have been shown to form organized lipid rafts both in culture and in animal-derived organisms, with physical properties similar to that in eukaryotic membranes. A recent paper published in PLOS Pathogens in January of 2013 utilized fluorescent and radiolabeled cholesterol to demonstrate that B. burgdorferi extracts cholesterol from the plasma membrane of eukaryotic cells, and that prokaryotic cholesterol-glycolipids can be transferred to epithelial cell membranes through both a contact dependent mechanism (using direct attachment) and a contact independent method (through released outer membrane vesicles). I highly recommend looking in to this story (maybe as a TWIM topic?), as it provides a shift in the thinking about lipid rafts, expanding their biological relevance to prokaryotes, and could have implications for the evolution of the eukaryotic cell membrane structure. Additionally, transfer of antigenic lipids from bacteria to host cells could play a role in pathogenesis - having multiple consequences for the host immune response and potentially contributing to heightened inflammation, and perhaps even direct targeting of the cells themselves by immune effectors. I’ve provided the citations and Pubmed link
s to a few papers on the B. burgdorferi story below, but also recommend digging into the story for H. pylori.

I’ve rambled enough for now, I should run – I’ve got to get to iTunes to write a good review or two…

LaRocca TJ, Crowley JT, Cusack BJ, Pathak P, Benach J, et al. (2010) Cholesterol lipids of Borrelia burgdorferi form lipid rafts and are required for the bactericidal activity of a complement-independent antibody. Cell Host Microbe 8: 331–342. http://www.ncbi.nlm.nih.gov/pubmed/20951967/

Crowley JT, Toledo AM, LaRocca TJ, Coleman JL, London E, et al. (2013) Lipid Exchange between Borrelia burgdorferi and Host Cells. PLoS Pathog 9(1): e1003109. http://www.ncbi.nlm.nih.gov/pubmed/23326230


Jennie writes:

Jennie Williams (RN) here - I've just seen something from Medscape that I thought you'd be delighted to know. An offering of clinical guidance on a successful recipe for Fecal Transplantation (bio-transplantation) for C difficile. Historical background on Fecal Microbiota Transplantation and a picture of success beyond C Dif to inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), idiopathic constipation as well. Fecal Transfer appears to work for C Dif that relapses as well.

Aside from fairly direct fecal transfers - this synthetic poo is described:
Elaine O. Petrof, MD, assistant professor, Department of Medicine, Infectious Diseases, Kingston General Hospital, Queen's University, Ontario, Canada, and colleagues created the human synthetic stool mixture by culturing the stool microbial diversity of a healthy 41-year-old woman and brewing a mixture of 33 different intestinal bacteria isolates in pure culture. They named the synthetic stool mixture RePOOPulate.

The bacterial mixture was infused into the colon of 2 patients in their 70s, both of whom were infected with a hypervirulent strain of C difficile, ribotype 078, and who had failed at least 3 courses of antibiotic therapy.

Both patients returned to normal bowel patterns in 2 or 3 days and remained symptom-free for 6 months. At that time, rRNA sequences representing the RePOOPulate mixture made up 25% of the gut bacterial population.

This link should get you to the right place.
http://www.medscape.com/viewarticle/779307

Thank you once again for making the world safe for microbiota Vince and friends!

Yours with warmest regards
Jennie

 

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