But where is the bacteria?
I meet Dr. Sandra Reuter, microbiologist turned bioinformatician. I find her work [so] fascinating, [sooooo] abstract (read between the lines…this is hard stuff). Sandra lives in Germany working at a university hospital. She explains, I have set up the sequencing here so that we can sequence anything of interest!
Bioinformatician’s combine biology, medicine and health-related studies with information technology. They collect and interpret data covering a range of fields. I gather Sandra’s focus is genomics, pathogens and microbial evolution.
Sandra jumps right in, Generally I am interested in all things bacteria, and especially those that cause disease. And I am interested in how they develop or evolve to cause disease, how they adapt. And lately, also how they move around a hospital system…I use whole genome sequencing to track these changes and adaptions in the genetic code.
In my PhD thesis, I worked on Yersinia. One of the species in this genus is Y. pestis, the plague bacterium, however I was more interested in a distant relative, Y. enterocolitica, that causes diarrhoea. There are different types of Y. enterocolitica, and I was looking into how they each came to be and what made them unique. I also then compared it back to Y. pestis, because both of them being pathogenic with similar markers could mean they both have a common ancestor that also had that trait. In fact, I found that they are not that related, and that they both came up with the same idea of pathogenesis seemingly independently!
I get so caught up in what she actually does as a scientist instead of what I need to focus on for my work. Before my brain has any sort of visual she shares info about superbugs, she simplifies genome sequencing (if this is possible) for me…talking family, ancestry, fingerprint, isolates, transmission chain of infection, bugs from different cities…etc.
The bug talk…one main chromosome, plasmids (extra bits of DNA), antibiotic resistance genes, quorum sensing. Sandra smells the plates, as the bacteria do smell slightly different depending on what they are and eat and which gases they produce (for some reason the latter brings memories of ceramic class).
I ask, do you have visuals, of any bacteria?
No she doesn’t have images of actual bacteria explaining she looks at bacteria in a different way…I draw phylogenetic trees ↓ to show their evolutionary relationships.
Sandra explains: This is a tree (spread-out view ↑) of different Yersinia species. On one side is what we call species complex (SC) 1 – pestis the plague bacillus, its close relative pseudotuberculosis, and also similis (as in similar to pestis and pseudotb). On the other side towards the bottom is enterocolitica (SC5), with different biotypes. In between: all the other environmental species, that don’t cause disease in humans but maybe insects (nurmii, entomophage) and trout (ruckeri). We compared it with the different biochemical tests used to identify the species (the red, blue, and grey boxes) and can see why some tests may be problematic, as they can’t tell species apart with confidence.
EMRSA-15 context: This ↑ is a tree (circular view)…EMRSA-15 isolate from around the UK. She explains details including computer use to organize information.
Though I am not expecting images of this sort and my mind isn’t really registering the content, I like their form and think they’re cool! I will use the circular (already established) format. Maybe I might (might!) bring in the first tree (spread out view).
She also explains gram stain which includes structure and color, something I can hold on to easily!
Gram staining is a way to colour bacteria. Under a microscope they are very tiny, so to see them better, we can put some colours on. And the behaviour comes back to how the cell wall is made up (structure!). The staining is done in several steps. In the first step, you use a purple dye (color!). Then in the second step you first fix the colour and then use ethanol to rinse them. Because the cell wall in Gram positives is thick, they retain the dye and are therefore purple. To stain the Gram negatives, you then use another dye in the last step, so they are red (another color!) in the end.
My last question to Sandra considers what is going on in the world these days, with the pandemic. Who will win? Microbe or human? She talks about both human and microbe becoming more or less aggressive. Both will win, she decides, each will adapt and continue…to survive. I like her attitude and appreciate the answer.
Going into the studio after our meeting, I look closely at the wonderful phylogenetic trees. I’m not certain I can replicate them by hand. (Oops! I really mean to say reproduce here but I’ll leave the word replicate!)
I let go of the bacteria I was hoping to draw via this sketch (note: it’s gram-negative!) so that I can figure out how to approach this next work.
On this particular day I think Gram-positive/Gram-negative. I see the yin/yang and the unplanned (but welcome) DNA strand that makes itself visible.
Finally getting clear, I will focus on Yersinia pestis, plague bacterium. I have an idea and head out to the map store to buy a map of the globe.
Sandra, it was good to spend a Friday morning speaking with you all the way in Germany! I can tell that you love your work! Thank you so much for sharing it with me.
More about → Dr. Sandra Reuter
Let’s see what I come up with for Y. pestis and the plague!
#flea #rattas #zoonotic #vector #reservoir #puzzle
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