A week of brain biggering

I got to spend last week in sunny California. I forgot how wonderful it is to sit and eat lunch outside! I was participating in a workshop held at the Department of Energy’s Joint Genome Institute (JGI). The workshop was entitled Microbial Genomics and Metagenomics. Basically I spent the week learning about different tools that are available to help biologists deal with the data flood that has come out (and continues to flow faster and faster) of sequencing technologies that continue to get faster and cheaper.

Since microbes are not exactly easy to observe with ones eyes, microbiologists rely heavily on genetic data to tell us about our organisms of interest. For environmental microbiologists, whose organisms can not currently be grown in the lab, knowing what genes our “bugs” contain tells us what processes they might be capable of and can also provide information into their evolutionary history. We can extract the total DNA out of a soil sample and begin to get a picture of what the community living within that soil is capable. However, before we do that we need to take the massive files of As, Cs, Ts, and Gs and figure out how to interpret that.

Imagine a text document of one of Shakespeare’s plays (or even a page of said play) with all of the spaces removed. Imagine each like cut out and shredded into a few random pieces. Imagine that you had 20 copies of that document and each was shredded differently. These multiple copies (or coverage in the bioinformatics world) allow you to attempt to piece together the play by finding pieces that overlap. This can be tricky if there are certain words or phrases that repeat frequently, but given the right computer program you can start to put some of the strips into larger phrases. This is referred to as aligning your sequences.

Once you have aligned sequences there are some tools available to search the alignments for segments that could represent genes. A genome that has been searched for known and recognizable genes is said to be annotated.

There is an interesting paradox here which is that technology keeps improving which means the volume of genetic sequence data we have to analyze is growing faster than the tools and programs we have to do said analyses, however the more bioinformatic data that exists the better our analyses will be because there will be fewer unrecognized genes and more organisms will be discovered. I can’t wait to see how archaic the program that I spent 5 hours struggling with today (ARB for anyone who is familiar… uggh!) will seem in 10 or even 2 years!

Comments

  1. #1 Mike Olson
    February 18, 2011

    Obviously if you knew exactly why, you’d be able to do something about it…but, why can’t enviro microbiologist remove their bacteria from the soil? And for that matter are the microbes you examine pathogens,or do they simply exist as part of an eco system and help maintain that system?

  2. #2 Dini Sohbet
    February 18, 2011

    Thank You…Imagine a text document of one of Shakespeare’s plays (or even a page of said play) with all of the spaces removed. Imagine each like cut out and shredded into a few random pieces.

  3. #3 Heather Olins
    February 19, 2011

    Mike, environmental microbiologists do separate bacterial (and archaeal) cells from soil (or water, or rock..) before extracting the DNA. There are various ways to do this, and depending on the sample it ranges from trivial to very difficult. Bacteria living in the environment tend to be very very good at attaching to various substrates. In fact I read somewhere recently that certain bacterial biofilms are better than teflon at being “un-sticky” – which can be problematic if they are pathogenic and the antibiotic doesn’t stick and get absorbed. However (to answer your second question) the vast majority of bacteria in the environment (and in your body) are not pathogenic at all.

    I hope this helps.

  4. #4 Mike Olson
    February 19, 2011

    Very much so. As to being pathogenic, is it possible that many bacteria are pathogenic if given sufficient opportunity? e.g. pneumocystis carneii? I don’t mean to be burdensome, but it brings to mind an early post by Kevin in regards to intestinal fauna. Meaning, that normally antibiotics are destructive to bacteria, but I’ve recently heard that antibiotics are being given to alleviate intestinal problems. This seems to be counter indicated unless you have an antibiotic which is very selective to a particular bacteria. Thus, it seems(and I grant this might only be an appearance and not a reality) that many human ailments are the result of normally non-pathogenic bacteria becoming opportunistic due to some unspecifed cause. I’m kind of trying to put all of this together as well as the notion of plasmids and how a bacteria share and pass on genetic info as needed. I’m actually not sure that there is an actual question there you can answer. It seems largely to me that the line between pathogenic and non-pathogenic is pretty blurry. And given that microbes can share, swap, drop, or use DNA as needed…it would seem genomics even in a straight forward fashion…in which it was easy to gather….would be pretty murky. Thank you for your time. If you see something in all of that you can answer…I’d appreciate it.

  5. #5 Heather Olins
    February 20, 2011

    Mike, you bring up an important point. While this is not my area of expertise, there are plenty of microbes whose location of the helpful-harmful spectrum changed in different environments. You are right that it seems the human gut is somewhere this phenomena often plays out. I don’t know what you are referring to about antibiotics being given to alleviate intestinal problems, but if for some reason the gut community got disturbed in someone and some harmful bacteria took over, antibiotics might bring that population down low enough to let the helpful bacteria re-establish. This actually gets into the realm of ecology and competition and colonization. Antibiotics aren’t going to kill everything that is present, but a broad spectrum antibiotic should hit which ever population is most abundant, and if that population is outcompeting the other populations, antibiotics could help re-establish a balance. I am mostly speculating here, and maybe Kevin knows more about what you are specifically referring to. I know that for most people, their gut community is much altered after taking antibiotics (generally lower diversity), but that after some time it returns to a community very similar to what was present pre-antibiotics.

    As far as sharing genetic information… some bacteria exchange plasmids and others do not. This also is not my area of expertise, but I learned something recently that I thought was fascinating. It actually seems that a lot of genetic information gets transferred from microbe to microbe via viruses – as they infect different bacteria they can bring along bits of DNA from one bacteria and deposit it in another. However, the role that these viruses play very poorly understood. I bet that the world of microbiology is going to see much more work on viruses in the next few decades (for this and other reasons).

  6. #6 Mike Olson
    February 21, 2011

    Kevin had a post in which a woman was developing progressively worse intestinal issues. To the point of a nearly complete physical shut down. I have a slight knowledge of medicine…nothing particularly strong…but I was under the impression that for most of these issues antibiotics were contra-indicated as when taking antibiotics for other issues one of the more disconcerting side effects is intestinal disturbance. In Kevins post, essentially the intestinal fauna of the womans husband was cultured and administered to her to restore a more normal balance of intestinal fauna. In that story it was indicated the doctor had tried a variety of antibiotics…which to me seemed a possible cause for greater and greater intestinal imbalance. But, I’ve recently heard that for irritable bowel syndrome(I cared for a Grandparent and ended up with variety of somewhat obscure knowledge about age related issues) there is a potential antibiotic response. All of that to give you which post I’d read and the reasoning behind my question.

    Now: To be frank, I’m very intrigued by the notion that virus’ might be transferring microbial DNA. Of course I’ve read a about about microphages and that seemed like a really neat trick of nature…as well as a potential means of treating illness(although I’ve heard this isn’t as promising as it first sounds)….But, I failed to consider that aside from destroying bacteria they might take some beneficient or at least non-detrimental path in regards to microbial genetics.

    I appreciate anyone who takes the time to pass along info as I’m not a professional in the field but am a very interested lay person. Thanks again.

  7. #7 Elyse
    February 21, 2011

    Were there any tools that focus on gene homology and function? I’m working with some genes that have only been shown to have a particular function in E. coli and whose homology was calculated through a string of organisms, none of which were tested for function. A similar problem is genes that are identified as being for cyanase, but were only tested in E. coli with cyanate, so may be for the broader category nitrilase. It’s hard to sort through all the organisms to find the original paper testing function, and then to compare homology only to those that are known.