The Joyful Microbe

This week we spoke with Justine Dees who is a Ph.D.-trained microbiologist, science writer, and the founder of the Joyful Microbe. The Joyful Microbe is a blog “where you can come to learn the coolest stuff about microbes, microbiology research, and being a microbiologist.” Read on to learn more about Justine and the awesome work she is doing.

What did your research focus on while you were earning your Ph.D.?

My research focused on Pseudomonas aeruginosa, which is an opportunistic pathogenic bacterium that causes many different types of infections, including cystic fibrosis, lung infections, burn wound infections, and chronic wound infections. I studied its antimicrobial resistance because it is a known "superbug," meaning it is resistant to almost all antibiotics on the market. But because we still don’t completely understand what makes it so resistant, I looked at the whole genome to see if I could find genes that were responsible for its resistance to so many different antimicrobials. I also studied its interactions with other bacteria, specifically Staphylococcus aureus, because they are commonly found together in chronic wound infections and can cause worse infections when they are together than when alone. Finally, I studied the differences between how Pseudomonas aeruginosa behaves in infections versus in a test tube.

Can you talk about the work you did as a postdoctoral researcher?

During my postdoc, I wanted to continue to focus on antimicrobial resistance because of its importance when it comes to treating patients — it is a huge problem that bacteria are becoming more resistant to antibiotics. So I studied the antibiotic resistance of the bacterial pathogen Haemophilus influenzae, which causes respiratory infections, by looking at all the genes in the genome to find which ones actually contribute to its resistance.

How did this experience inspire you to start the Joyful Microbe?

I have had a passion for microbiology since my undergraduate years studying biology. My plan was to get a bachelor’s in biology and then become a cancer researcher. That was until I took my first microbiology course and realized that bacteria were what I wanted to focus on and what I was passionate about. After taking microbiology and having an incredibly engaging professor that told stories about his background in industrial microbiology, I became interested in all the things that microbes can do for us. I also wanted to cure infections and understand antibiotic resistance.

During my studies, I always enjoyed talking to my friends about microbiology, whether they were a microbiologist or not. I've always had a passion for trying to break things down into simple, easy-to-understand ways. It gets complicated really fast when you're studying something at the Ph.D. and postdoctoral level. It's easy to get bogged down with all of the complex technical stuff after you learn it, but so many of the general principles in the world of microbiology are fascinating and worth sharing. Then I thought, I’d really like to have a platform where I could share about microbiology in a simple, non-technical way so that anyone can understand it. The blog has opened up so much more of microbiology for me because when you do a Ph.D. and a postdoc, you narrow in on one tiny aspect of your field and become an expert in it. But there's so much out there that is amazing and cool. And it’s given me a chance to explore those areas as well.

Since I focused on pathogens for all my research, I wanted to take some time to better understand the positive side of microbiology. I think many people don't realize that most microbes are not harmful, and many of them do good and helpful things in the world and for us. For example, they help us make fermented foods. So, I did a series on fermented foods where I interviewed experts in the field. It was fascinating to be able to take a deep dive to better understand the role of microbes in improving and preserving our foods.

You are passionate about sharing science and microbes with the general public. Why do you think this is so important?

I believe that sharing science and microbes with the general public is important because microbes impact pretty much every aspect of our lives. However, most people don't think about it that way. If they do think about microbes, it's about the ones that make them sick and then they get hyper-focused on disinfecting and sanitizing. That's understandable, I can say that I've definitely been there and thought about microbes in that way. Even when people first learn about making their own fermented foods, it’s easy to have a fear of pathogens making you sick. But, amazingly, pathogens are not something you really have to worry about with fermented foods because the fermented food microbes preserve the food and prevent foodborne pathogens from growing. But without that knowledge, then there's just fear because it’s the germs that make the news, rarely beneficial microbes.

I really want people in the general public to not worry so much about microbes and have a little bit more freedom to live well with microbes. If you are constantly disinfecting and sanitizing — which right now, of course, is important because we're in a pandemic — and flippantly using antibiotics, then we are going to harm ourselves and the environment in the long run because of the resistant pathogens that can evolve as a result of our overuse of antimicrobials. So, it's important so that we're not harming ourselves, but it's also important so that we can enjoy our lives a little bit better, not living in fear, but understanding the microbes that are bad and then enjoying the good ones.

Are there specific techniques or tools you use to make the posts you share more interesting and digestible to your audience?

I try to remember which words are jargon — technical terms — and not use them, to begin with. But in cases where I need to use jargon, I define the words. I also try to avoid using complex non-scientific words and use simple words because if I have to include jargon, I want those to be the complex words. I want anyone to be able to read what I write and not have trouble with the words that don't even have anything to do with the science. I also try to ensure that my sentences do not go on and on forever because that makes it harder to read, in general, and people will lose interest. I actually created a science communication guide that explains some of these strategies for anyone who is interested in improving their ability to communicate science clearly and effectively.

Do you have any advice for someone who wants to start distributing their research work in a way that appeals to a broader audience?

There are multiple ways researchers can distribute their work to a broader audience: 1) start a blog, 2) start a YouTube channel, and 3) share on social media (Twitter, Instagram, and Facebook).

I firmly believe that it's better to share information through a blog and then share the links on social media platforms if you are in it for the long run. If you start with a blog post, then you can format the piece the way that you want to and cite sources. You could also create YouTube videos to share your research and embed the videos in a blog post. As for social media, many people interested in science are on Twitter. And once you gain over 1000 followers, you start to reach people in the general public (there was actually a study in 2018 that showed this). And so that's pretty awesome because if you build up a following on Twitter, you can start reaching a broader audience just naturally through sharing your work on there.

Do you have a favorite microbe that you have written about?
Honestly, it’s tough to choose a favorite microbe, and I'm a very loyal person by nature, so I always name Pseudomonas aeruginosa as my favorite microbe because I really loved studying it for my Ph.D. I spent the most time with it in the lab, got to know it well, and think it's super interesting. It's scary because of its antibiotic resistance — it's a superbug — but it has these crazy interactions with other microbes that actually make it cause worse infections than when it’s alone. It's like that boogie monster that's fascinating because it’s scary. But then it's also beautiful. You can look at pictures of it online, but it makes these really lovely pigments: blue-green pyocyanin and yellowish pyoverdine.

But I also have to say that Streptomyces species of bacteria are on my list of other microbes that I really love because they make antibiotics. So they're the antithesis of the superbugs that are super resistant to antibiotics. There's this whole warfare that's going on between microbes. They make antibiotics against each other, but we've taken advantage of that and been able to isolate antibiotics for ourselves from these microbes and use them to treat infections. And so Streptomyces are soil bacteria that make antibiotics. I got a chance to work with them during my Ph.D. when I taught an undergraduate research lab called the Freshman Research Initiative, a course-based undergraduate research experience (CURE). The students isolated antibiotics from Streptomyces from the soil. I thoroughly enjoyed being able to see the students isolate bacteria for the first time, find species that made antimicrobials, and then discover if those antimicrobials were effective against pathogens. And so I have a fondness for Streptomyces because of that experience and because they are an excellent example of microbes that help us.

How has the COVID-19 pandemic impacted your work with microbes? Are people more interested? More afraid?

The COVID-19 pandemic has impacted my work. I think a lot about it when I’m deciding what I feel is appropriate to cover on the blog at this time. I believe that it is important not to take away from the message of the importance of fighting the pandemic, but I also don’t think that I need to stop talking about the positive impacts of microbes. So, I wrote a blog post about “understanding microbes during a pandemic,” where I interviewed several microbiologists to get their opinions on this idea of how the pandemic has impacted people’s views of microbes how we can help people not be afraid. I think people are interested, but I think they're more nervous and afraid right now. To be honest, I am too. And that's not a bad thing, because we need to be careful during this pandemic and be smart about the way that we live our lives right now. But at the same time, I don't want people to live in total fear. I want us all to have a good relationship with microbes and remember that there are beneficial microbes out there helping us. So, the pandemic has actually encouraged me to communicate more about the positive aspects of the microbial world. I'm not a virus expert, and I'm certainly not a pandemic expert, but what I can do is try to help people have a balanced view of microbes despite this pandemic.

We know that sourdough starter is very trendy right now, can you briefly explain what’s going on there from a microbial perspective?

Sourdough starters begin when you mix flour and water together, and over time, a community of microbes begins to grow. You are actually cultivating microbes that are from the flour, the environment, and from you. When you have an active starter, you end up with bacteria and yeast living in a symbiotic community in this flour and water mixture. The yeast is responsible for making the dough rise because it creates carbon dioxide bubbles that provide the fluffy texture of the bread. The bacteria are mostly lactic acid bacteria that are responsible for the distinct sour flavor and smell of sourdough bread from the lactic acid and acetic acid they make. To learn more, you can read the blog post I wrote about sourdough starters.

Anything else you would like to add?

There are lots of different things that you can do to acquaint yourself with microbes if you don't feel completely comfortable with them. One of those activities is to create a Winogradsky column, which is a mixture of mud, water, a sulfur source like an egg, and a carbon source like paper that you put in a clear container. You can also experiment with adding other things like different metals, carbon, or sulfur sources and varying the amount of light. What happens is the microbes in the mud are selected to grow because of the ingredients/conditions you supply, and you get this interesting set of colored layers from the different microbes growing. I think that it's not a very scary thing to do and probably even more approachable than at-home fermentation simply because all you're doing is mixing together mud with paper and water and egg and some other stuff and watching it transform over the course of a couple of months. You can see some beautiful photos in the blog post I wrote about Winogradsky columns. It's a really neat activity that you can do with kids, or just do it yourself. It doesn't matter — it's for anybody. I love that it is a visible representation of the microbes that we normally don't see. Also, I've created a workbook for anyone who wants to try this out. You can download the workbook and track your Winogradsky column over the course of the eight weeks. The workbook guides you through what to look for, including bubbles, layers, etc. This activity is a great way to get comfortable with the microbial world or teach your kids about the different microbes that live in the soil and water that we usually don't even think about being there.

A huge thank you to Justine for taking the time to speak with us! If you want to keep in touch with her you can check out the Joyful Microbe and her website. Now, I am off to create my Winogradsky column!

Some responses have been editing for length and/or clarity.

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