Itzik Mizrahi Lab - Microbiology Research Group

Mizrahi lab - Microbial Ecogenomics

The circularity of David’s life

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I’m David, in my second year of postdoc in the lab, and my problem are plasmids.

To tell you how I got there I need to explain a bit. I did my PhD in a molecular evolution Lab with Prof. Tal Dagan in Kiel university, Germany. Back then we were interested in the evolution of specific genes. What always became a topic was horizontal gene transfer (HGT). Microbes are able to transfer DNA from one cell to another and thereby exchange functional genes, one way to do that is via transfer of a plasmid. There we go. Plasmids are circular genetic entities, usually shorter than genomes that can encode functional genes and have the ability to move between cells. Many of you might know them as tools in microbiology to transform bacteria and have them perform various new tasks related to genes on the plasmids that can be selectively expressed. Also in public health plasmids that can transfer antibiotic resistance genes are a hot topic since years.

 

What is it about?

 

Back in Kiel we were interested in questions like: Do paralogous genes stem from gene duplications or horizontal transfer events? Now that I joined an ecology lab we can see things from a broader perspective. We would like to ask questions like: How does Horizontal gene transfer, that is mediated by plasmids, influence the evolution of entire bacterial communities. From the perspective of a gene to the perspective of an ecosystem.

In our Lab we work with Microbiomes, the bacterial communities associated with specific environments. In my case this is the bovine rumen and the human gut. Metagenomic sequencing allows us to capture all the DNA in an ecosystem. We can look at Bacterial species using 16S amplicon sequencing, ask questions about gene functions, and even reconstruct microbial genomes from the metagenome. But to find out which genes are mobile, and can be used by more than one microbe, we need to look at the mobile genetic elements, the plasmids. So we needed a tool to assemble plasmids from the vast and messy metagenomic reads.

 

 

The Recycler:

recycler

We worked with Roye Rozov and Ron Shamir from Tel Aviv University on a Software that  assembles plasmids from metagenomic reads using a graph based approach. Details can be found in the Publication itself. The innovative logic is best explained in my opinion by a ride through a round of recycler: Metagenomic reads are assembled into contigs, using a generic de novo assembler (e.g. SPAdes). Shared k-mers between these contigs tell us which of them are connected in reality, forming bigger genetic entities. This connections create what is the assembly graph.

 

fig-1

Now a plasmid will in many cases not entirely be assembles into one contig. Most likely it consists of multiple parts that are connected. Since a plasmid is also circular, it should appear as a circle in the graph. Several contigs connected in a circular way. Moreover, if these stem from the same plasmid, all parts of it should be equally abundant. Imagine a photo of Paris (metagenome) that is cut into a 1000 piece puzzle (reads). If you now look at the roundabout (plasmid) around the Arc de Triomphe (the place where hundreds of German tourists spend half their weekend because they chose an inner lane and can’t get out anymore), You will see that all puzzle parts (contigs) that contain pictures of the circle are connected (k-mers) and you will see that each part exists only once, since this place exists only once in Paris. If there were two identical ones, each part would be there twice and so on. This is how a plasmid is found.

 

Another part is that some plasmids might share a part. Both have this identical region. In this case, the graph would resemble a shape of the number 8. And the shared part would be found as often as the parts from plasmid A and plasmid B. Let’s lay there are 5 plasmids A and 3 plasmids B, the common contig would have an abundance of 8 since it is present in all of them. Also this can be recognized by Recycler, and both plasmids will be assembled.

 

 

What can we do with it?

 

It allows us to study the plasmidomes of ecosystems (all the plasmids present in an ecosystem). We can ask questions about which genes are encoded upon them and therefore mobile. Speaking of mobile elements, we can use it as well to assembley the genomes of viruses, as long as they are circular and consist of DNA. Adding too many further details would be a bit of a spoiler here. You’ll read that after you summer holiday in an interesting paper. You wouldn’t want George R.R. Martin to tell you the plot of his next novel either, right? And science is at least as in interesting as that. Think about what you would do if you knew the sequence of all plasmids in an ecosystem? What would it be?

 

 

Think big into the future (What can we do with it for Sci-Fi fans)

 

Now what we can talk about is, what research like this can enable us to do in the far future. Specifically, I find it really inspiring to think about application that could be derived from such research and really change something for the better. Did you read Goor’s blog entry? You should! He is talking about the option to engineer the rumen microbiomes of cows in order to decrease methane emission and optimize energy harvest from their feed in order to allow for a more sustainable livestock agriculture. What if we could change the microbiome by inserting plasmids into the bacterial populations that supply the right bacteria with the needed functions to more efficiently harvest energies from their feed? Or think about people that suffer from chronic bowel diseases such as Crohn’s disease or ulcerative colitis. These diseases have been found to be connected to the microbiome, and maybe the functional  alteration of the microbiome via plasmids could be a novel way of treatment.

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