Hello, this is Andrew, Lee and Nabil from the Microbe Info podcast. And we're
going to tell you about our microbe moment. OK, so that's what is your favorite
microbe? That's a hard one. There's so many to pick from. Does it have to be a
pathogen? I'm going to say no, and I'm going to go with Thermus aquaticus as my
favorite microbe. That is an extremophile that produces TAC. And we use that in
PCR almost all the time. And without PCR, I don't have a job. So thanks, Thermus
aquaticus. And is it what's an extremophile like? Is that some kind of racist?
No, it's not like. Yeah, it's not a political extremist or anything like that.
It's a it's a microbe that lives in an extreme environment. So Thermus aquaticus
lives in in hydrothermal vents, kind of places we wouldn't go. Cool. As you can
tell, I'm not a microbiologist. I'm just a lowly computer scientist who's fallen
into this field. But Lee, maybe, you know, a bit more. So what's your favorite
microbe? I like to go with Neisseria. Gonorrhea? Any of the Neisseria, actually.
So it's a whole genus of microbes, of bacteria. I like that they can just like
soak up DNA from other Neisseria, like whenever they feel like it. It's kind of
interesting. And they recombine like all the time. And they're just kind of a
fun study. And maybe I'm just a little bit biased. That's just where I started
off in public health. I think everyone remembers their first microbe. Yeah, I
did a bit of E. coli blasting. That was kind of my first introduction to it. I
didn't even know what E. coli was back then, you know. Wow. Well, Andrew, have
you ever had like someone say like blah, blah, blah, this bacteria and you're
like, whoa, I'd have no idea that it even existed. All the time, people come up
to me and say, oh, yeah, did you hear about this? You know, it's like in the top
three pathogens, you know, on food. And it's like, really? I've never even heard
of it. Don't even know how to pronounce it. You know, it's it's a bit crazy.
But, you know, so many of them out there like. You only hear about the deadly
ones, you know, to really cause high mortality, but you don't hear about the
ones that cause, you know, a dicky tummy or things like that. Those are less
important. I think some microbes have slightly better marketing budgets than
others, really. Like Shigella. Yeah, Shigella. Don't get in Shigella's way.
Yeah, it's just it's just E. coli, isn't it? You know, with a bit of a plasmid.
Is it even worthy of a name on its own? Not really. I mean, it's just it's more
or less, therefore, because, well, we'd have to change all of the monograms
because it's not worth it. Taxonomy, the oldest argument in history. If it ain't
broke, why fix it? OK, so what's the coolest fact you know about microbes, Lee?
One of the coolest things about Listeria is that people are starting to use its
tendency to infect people intracellularly. And so over the last 10 or so years,
kind of under the radar, almost some pharma companies are sticking cancer genes
on them, like a mesothelioma cancer gene, let it infect and then present the
mesothelioma gene and actually have a sort of vaccine against cancer. So that's
one of my favorite things about microbes right now. Wow. That's kind of cool. I
think for me, one of the favorite things about microbes is they make all of my
favorite foods. I couldn't have any of them without microbes. We all know the
obvious ones like, yeah, you need yeast for bread. You need it for beer and you
need you need lactobacillus, sweet yogurt and all of that. But did you know you
needed microbes to make chocolate? What? Yeah. Chocolate is a is a partially
fermented product. So, yeah, if you if you didn't have like a bit of yeast and a
bit a couple of bacterial species in there to to help try to chug the cocoa
along, good enough chocolate. Well, what I like is FMT. So if you can microbiome
transplants and you give someone a bit of poo and you know, if they've got C.D.
for whatever, in most cases, they're cured within a few hours. You know, after
probably having spent months and months and months taking antibiotics. And for
the most part, we don't really know why it works. We don't know which microbes
are helping or not. And it's a big mystery. But we do know that it's a load of
microbes. A lot of different species are actually helping out and fixing people
very quickly. So we all need a bit of poo in our lives. OK, what do you think?
Do people take a pill on that or do that? It's hard. People generally the way it
goes in is down a tube going down or a tube going up. And it usually involves a
blender and a brown soup. Oh, yeah. That's rough. Yeah. And usually the best
donor is actually someone in your own households. Interesting. Yeah. You
discussed that with your wife. One time I did donate my stool and it was it was
not an experience I would do again, probably, but for research internally. And I
and I hope to to hear more about that sequence one day or analyze it myself if I
sneak into the files, if they they probably don't have those open anymore. Sad.
Well, do you remember Aaron Darling was sequencing every nappy from his his kid
for the first few months of life? Yeah. The nap, the diaper. Yeah. Publish some.
Well, we don't get published. It's just it's just his own little thing. I think
it's a PGM as well. That's back in the day. Incredible. I don't know. OK, so
Nabil, how did you get into microbiology and why do you stay? I wanted to do
work with genomics and I wanted to do bioinformatics and my doctoral advisor
told me that, well, bacterial genomes are really small, so they should be
easier. And I was like, yeah, makes sense to me. So there we are. Rational
choice. And Lee, what about you? I was I was getting into a new field of
bioinformatics and I didn't know what I was doing, and then somebody from CDC
cold called my lab. Told us, hey, you want to work on Gono and you're like,
yeah, OK. Almost. Almost. He said we sequenced four genomes, some of the first
genome sequenced at CDC on the four or five, four. And they're nice, Syria,
meningitis. And your lab has by competitions. Can you analyze this for us? And I
was the next PhD student. That's how I got into it. And I and I stayed because
it's so incredibly interesting. And that and we have a nice impact. Well, you
Andrew, I'm a computer scientist, so I accidentally fell into this area and
couldn't escape. Why do I stay? Well, now that I've specialized in an area, I
can't escape. They tell me, yeah. So I was doing limbs development. In the
Sanger Institute, and then I went into a pathogen genomics team, but doing more
infrastructure work, you know, like back end database, that kind of thing, and
then over time, I discovered that, you know, at lunch, we would be having all
these conversations about like STIs and and these horrible foodborne pathogens.
And it was a pretty normal day, you know, to discuss these kind of things. And
then I realized, hang on a sec. I've changed fields without realizing it.
Interesting. And I've never looked back. OK, so what do you think is the biggest
misconception about microbiology and what would you like to tell people who
think this misconception is true? Lee, do you wear a white lab coat? Oh, that's
a good one. No, I have pictures out there wearing a white with me wearing a
white lab coat for fun. But we do not wear white lab coats as bioinformaticians.
Have you ever been photographed in a pristine white lab coat for petting water
or buffer for a photo shoot? Yes. Yes, I have. So have I. But I would but but I
was I was an undergrad actually pipetting things. I was actually doing that
stuff. But wait a minute. You were someone to that with you. You are a computer
scientist. I was photographed. I think I was wearing a green lab coat, actually,
which meant I was a danger to everyone else in the lab. And so I was petting
buffer into a used nanopore flow cell just to prove that, you know, I could do
the nanopore stuff. I got photographed by petting for a mini prep. I was doing
an actual mini prep for a nice area, even in Jedidus one time. I was doing it,
but I don't know. Like, what did they use your photo shoot for? This is still
still like you're you're a computer scientist. It's to prove, you know, that we
we know our stuff, you know, and not nice photos for presentations. Interesting.
I want to see if Nabil ever had that, too. No, never. I don't have any of those
sort of photos. Hmm. Well, I do have a white lab coat. I think Nabil probably
has one as well. I don't think I ordered a new one when we moved to the new
building. What you do is you walk in and you take anyone in your size. OK, put
it on your hanger. I've got a hanger.  when it's going into the lab. I've made
it. Yeah, it's about time for you to get your picture, Nabil. Yeah, yeah. That's
a good misconception. Yeah, I don't think the lab coats we use generally are
white. They're usually blue. Well, they're graffitied often, and they've been
washed many times. Yeah, if they're white, they're definitely like this off, you
know, gray. Yeah, the pristine white ones are for PR purposes. You know, they
have a beautiful logo on the side, and they've been worn once, and then they're
put back. Never used for real lab work. We use those for like when TV crews come
in. Okay, here's another one. Have you guys ever analyzed a double helix of DNA
rotating on your computer screen? I wish I had that graphic. Like the Matrix? Or
like in the Matrix? The crazy thing is sometimes, you know, you look at DNA
sequences, and you will know just from looking at the sequence or from like a
GFF file scrolling by, oh yeah, that's what it is. Yeah. After a while, you get
to know all these things. Agree with that. I think dumbing to BAM files, you get
a bit of that. Like MPilot, we just kind of watch the pileup move over the
screen. Yes, yes. Oh, that's contaminated.