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Human Skin Microflora: DNA Sequence-Based Approach to Examining Hand Disease by Dr. Julie Segre
But if you examine the sequence of the 16S rRNA, the ribosomal RNA which is shown on the left here, what you see is that it actually has these stem regions which form a lot of double stranded basic base pairing. And from those, that actually puts a fair amount of conservation constraint on those base pairs. And then there are the (loop) regions which are more variable. Now, when we look at the sequence of the stem regions, those are conserved. And that serves as what we consider an evolutionary clock. So if we looked at the conserve regions we can say well there is some change in them, but that allows us to say this is a staphylococcus, this is a streptococcus and assign what type of bacteria it is.
The sequences in the loop region will change even faster than that. But these sequences of the 16S gene allow us to identify what type of bacteria it is. So the orange highlighted sequences are how we amplify this gene out of a bacterial genome and also we use the purple sequences. Those are highly conserved and then we examine the intervening sequences. And that allows us to identify what type of bacteria this is.
Now here I show you an example of how we compare the data that we obtained with our DNA survey sequence identification with our culture methods. So what we did here was he had healthy volunteers come in. And we looked at two different sites of them. And actually we did 20 different sites of them as you will see. But I am just showing you the examples of two different sites here – from the face and from the belly button. Now, on the right side of each bar graph, you see what we found when we brought these swabs down to the (microbiology lev) and tried to culture everything that we could.
Well the dark blue is called propriona bacteria from the face. And that is an oily loving bacterium. And so the skin is a little bit oily and that would make sense that those are the types of bacteria that live there. As well as the orange is the staphylococcus. That is like staphylococcus epidermidis which is one of the most common healthy bacteria that we can grow.
And if you compare what we found on the face from culturing versus survey, you can see that we did a pretty good job, but we completely lack the cornflower blue and the lighter blue. Those are actinobacteria and you can see the chart on the right hand side. We failed to culture them.
These bacteria are actually the (carinobacterium) and other actinobacteria are very hard to culture because they take – they are very slow growing. Sometimes we grow them after about six days. But by six days, the staff and the propriona bacterium grow so well that they have almost overgrown the culture plate.
And you see this even more when you look at the samples that we collected from the belly button of this person. Well culturing it seems like the orange and the red are the firmicutes. Those are the staph and the strep and other bacteria that fall under the greater taxonomic name of firmicutes. And, so that is what we can culture from this person. But when we look at the survey, what we see is that really 50% of the bacteria are the (carinobacterium). And as I said, we just had a very hard time culturing them.