Understanding microbes during a pandemic

The coronavirus (COVID-19) pandemic has undoubtedly changed our perceptions of microbes in our daily lives. This virus is on our minds all the time. And having microbes regularly on the mind is likely a new thing for many. It’s easy to become overwhelmed by it. On the one hand, it’s good to remember that microbes are there, so we maintain proper hygiene and cleanliness. And right now, it’s good to be extra careful.

But my concern, as a microbiologist, is this pandemic will leave many with a highly negative view of microbes. Maybe it will be an increased fear, or maybe it will be simply hating microbes altogether. And I think it is important to have a balanced understanding of microbes: knowing about the bad ones (germs or pathogens) and being careful as a result but also appreciating and enjoying the good ones.

So, this post is a discussion about our view of microbes in light of the COVID-19 pandemic. I asked four microbiologists for their thoughts on how this pandemic is affecting our relationships with microbes and how we can ensure that our view of microbes is not strictly negative through this pandemic and into the future. You will see that — despite us all being microbiologists — we have differing points of view on this subject.

How will COVID-19 affect our view of microbes?

Mark O. Martin: Clearly, the emphasis on handwashing and sanitation of surfaces will bolster the view of the microbial world as uniformly negative and somehow “unclean.” I also think that the myriad beneficial impacts that microbes provide us will be less noticed. On the one hand, I understand this given the news, but it is a view that does not reflect a balanced view; our world is inescapably microbial.

Maureen Berg: As a microbiologist who has spent 10+ years in a lab using aseptic techniques, I’ve been trained to be constantly aware of what I touch and potential sources of “contamination.” In my daily life, while my brain still is highly aware of microbes, I don’t worry about “contamination” most of the time because most microbes are harmless to us. I think COVID-19 will make people more aware of those sources of “contamination” (e.g., fomites), but the panic about “germs” will only be temporarily heightened. I am more concerned about misunderstanding of certain terms; for example, the use of “herd immunity” with the UK’s COVID-19 strategy might make it harder to convince people to vaccinate themselves and their family (since herd immunity is the reason why vaccines are beneficial for the community).

Mo Kaze: It’s hard to say. Viromics is still a relatively recent field, and we, scientists, still have a lot of basic knowledge gaps to fill in on the topic. I have already seen the whole spectrum from terror to blasé regarding COVID-19. It’s too early and scary right now, and that makes it really hard to think about the future. Being worried about being negatively impacted by COVID-19 is a rational concern for front line and essential workers, and it is completely reasonable. 

I hope we can get somewhere close to a healthy appreciation for infectious and disease-causing microbes. I hope that we can engage in thoughtful reviews of our behaviors that lead to widespread viral transmission.

We take for granted the use of antibiotics, and antimicrobial resistance is, unfortunately, a player in the COVID-19 treatment and post-treatment care. I hope that the eventual development of a vaccine for COVID-19 will renew faith and support for vaccinations and caring for the other members of our “herd.” I hope that antibacterial resistance is taken seriously, and an educational push and research are funded. I see a lot of hope in the use of viruses for treating antibiotic resistance and potentially to fight other diseases.

All the handwashing education has been great! I’m so curious to see what bacterial infections crash in prevalence due to the increase in preventative measures.

Scott Chimileski: I think that COVID-19 has raised the public consciousness that microscopic entities exist all around us, which might be seen as a positive; however, any positive impact is greatly outweighed by the fact that this particular virus is harmful or lethal to ourselves and our loved ones, and has impacted many livelihoods and life plans. I think this fear is justifiable and probably necessary, given that we are experiencing a pandemic the likes of the Spanish Flu 100 years ago. The way to counteract the fear is simply through education about the virus. If everyone knows how to kill the virus with soap — what the virus can and cannot do — this knowledge is empowering.

What can we do to help prevent a significant increase in fear of microbes?

Mark O. Martin: I think it is important for the public to recall a few things. Words matter. For example, the term “germ” had utterly no negative connotation when Pasteur popularized it during his battles against the concept of spontaneous generation. I even did a talk at ASM last year about this that was recorded. 

In a similar way, have a look at the Wikipedia entry here for mysophobia (verminophobia, germophobia, germaphobia, bacillophobia, and bacteriophobia, etc.). These are all terms associated with “germophobia,” a genuine psychological condition, as explained in the entry. But notice how often microbes are associated with “dirt” and other supposedly negative terms.

The fact is, microbes that cause disease are very rare. Think of them like the “juvenile delinquents” of the microbial world: small in number, but they get ALL the press.

Maureen Berg: I honestly think the extra panic and fear about microbes will subside in a year (or so) once the outbreak is no longer in recent memory. However, even when we don’t have an ongoing pandemic, I think most people don’t appreciate microbes and how important they are in everything. Beyond food microbes (which are cool, but there are other cool microbes), I think educating people about how diverse they are and how integrated microbes are into our ecosystem is one way to increase microbial appreciation.

Mo Kaze: We have a significant educational gap that needs filling! I have seen a lot of confusion and misunderstanding about viral infections and spread, and this is where investment in quality, scientific, evidence-based public health information is needed. We need to give well-trained, qualified scientific communicators or interpreters platforms with a wide reach to increase understanding in a non-judgmental, health-first fashion.

Scott Chimileski: I don’t think that we should do anything right now to help counteract an increase in the fear of microbes. I say this because the pandemic is still very much unfolding. In a way, the main countermeasure to slow the spread of the virus is a fear of microbes — to avoid contact, keep your environment extra clean, etc. When there are so many real and serious impacts of the virus currently on lives and livelihoods, I just don’t think such an effort would be appropriate or effective at this time. When it comes to life and death, I believe that most people are reacting in an emotional and visceral way, and now is not when people are primed to receive a purely rational appeal for microbes that is based on the fact that most microbes are harmless or helpful. I think it would be best to let the pandemic fully play out, for people to remain vigilant with countermeasures. There will be another time to convince people that microbes are not all bad!

What are some examples of microbes providing a benefit for us?

Mark O. Martin: All you need to do is look in your supermarket! So many foods have been processed or created by microbes, ranging from yoghurt to sausages, from cheeses to tofu. Some microbes, like Xanthomonas campestris, make a suspending agent (xanthan gum) that is in pretty much all bottled salad dressing!

Look at the way that bacterial viruses (bacteriophages) are now being explored as therapeutics against bacterial infections in humans. My beloved predatory bacteria also pursue and consume other bacteria. And the vast majority of antibiotics are produced by microbes!

But let me get still more basic. I tell my students each year to remember that the two most important enzymes on the planet, Rubisco (that converts inorganic carbon dioxide into organic molecules) and nitrogenase (that converts practically inert nitrogen gas into bioavailable ammonia), are both BACTERIAL enzymes. Without microbes, our entire ecosystem would fall apart!

Maureen Berg: A lot of food products are possible only because of microbes (yeast, cheese bacteria, etc.). Microbes are also crucial players in global energy cycles (carbon, nitrogen, etc.).

Mo Kaze: Microbes can do everything, and they DO everything. One of my favorites is our dear old friend E. coli. We have loads of E. coli along our gut tube, and it makes vitamin K and B-complex vitamins. We can’t make vitamin K, which is actually a group of different compounds, on our own, but we need it for really important things like making scabs! Imagine if you got cut and couldn’t form a scab. That sounds awful to me. I deeply appreciate our helpful gut microbes, especially E. coli! In the environment, there are microbes that can help take compounds that make up greenhouse gases out of the air and hold on to them. I appreciate all the beneficial things microbes do for us every day. (I also enjoy the wine and bread and kimchi we wouldn’t have without them).

Scott Chimileski: There are so many! I thought deeply about this subject of the balance between harmful and helpful microbes a few years ago around the launch of our book Life at the Edge of Sight. These thoughts were distilled in an op-ed in STAT titled, Microbes Gave us Life. In that article, we included a top list of positive impacts of microbes. “…microbial life illustrates an intrinsic duality in nature. Microbes make some of the most delightful things on the planet, like wine and chocolate, and they are capable of unimaginable devastation, like the Black Death.” 

Do you have any other thoughts to share about how we view microbes in light of COVID-19?

Mark O. Martin: I yield to none in my love of the microbial world. But I am certainly washing my hands thoroughly in soapy water, coughing into my elbow, not touching my face, and generally following the CDC suggestions. It’s just important for the public to understand that our entire planet depends on the microbial world within us and around us. The ones that hurt or frighten us are a small, small percentage of the microbial wonders everywhere!

Maureen Berg: I just hope people actually continue with the handwashing habits that they’ve developed during this pandemic. While I don’t worry about most microbes (I mean, if I drop pretzels in the dirt when hiking, I’ll still eat them with little concern), I do wash my hands a lot, especially if I’ve been out in the public with a lot of other people touching a lot of common surfaces. Handwashing is so incredibly effective in preventing many illnesses. They say that microbiologists are either extreme germaphobes or they will eat food off the floor; I think most microbiologists have a fairly balanced view of microbes: they worry about a few (pathogens, mainly), but outside of those specific situations, they’re happy to be covered in microbes. In an ideal world, this sort of balanced view is the norm in non-microbiologists as well (i.e., know when to be a germaphobe). Right now, people are learning how to be (better) germaphobes, but I think once this pandemic passes, then it’s important for us to remind people how most microbes aren’t harmful.

(Also just as a side rant, it’s great that people are getting better at handwashing and stuff, but many are still terrible germaphobes (i.e., not realizing how many common surfaces they touch during the day, and you gotta wash your hands after touching those right now!!!))

Mo Kaze: I hope that we’re able to introduce and offer more microbiology education for the public. The invisible nature and frightening outcomes of some opportunistic microorganisms make it harder to counteract fear. I hope that people will want to understand more about viruses and how they act in the environment, in our own bodies, in bacteria, in food, in the soil, well everywhere. I hope there’s support for funding for more research in viruses and education about them. Just like bacteria, there are good ones and harmful ones. Bacteria have taught us so much about our own biology, and I know that more viral discoveries will do the same.

Scott Chimileski: I think that the best distillation of my thoughts on the subject are from the STAT op-ed! My thoughts have not changed much since then — and this is very much relevant to that article.

Summary

• The COVID-19 pandemic — that we are all going through right now — has made us highly aware of microbes in our daily lives.
• An increase in fear of microbes is understandable and, in some ways, helpful in keeping us healthy and safe right now.
• It is likely that with the increased awareness of microbes, handwashing practices have improved.
• Microbiologists have differing opinions on whether or not we should emphasize the benefits of microbes during this pandemic.
• Microbes provide an overwhelming number of benefits (fermented foods, sourdough bread anyone?) in our lives and on this earth, and I believe we should not forget this whether or not we are going through a pandemic.
• Let’s remember that not all microbes are germs.
• The benefits of microbes, however, should not justify unsafe behavior during any pandemic.

Bios for the microbiologists who provided their thoughts

Mark O. Martin, PhD, is an associate professor of Biology at the University of Puget Sound in Tacoma, Washington. There, he teaches Microbiology to seniors, and Introductory Cell and Molecular Biology to freshmen. He also has an undergraduate based research program that studies bacterial predators, as well as bacterial associations with animals of various kinds.

Maureen Berg, PhD, is a Postdoctoral Scholar at the Joint Genome Institute, where she studies viruses that infect bacteria. Her graduate work focused on understanding the microbes that live in the guts of soil nematodes. She resides in Berkeley, California with her snake Hank and her slime mold Cheesecake.

Mo Kaze is a fellow at the Joint Genome Institute, a seasoned microbiologist, and soon-to-be PhD. She loves all things viral, bacterial, and archaeal, and if she’s not thinking about microbes, she’s probably thinking about dogs. Her podcast, SurfaceLearning, with fellow scientist Maureen Berg, explores all the weird and wonderful things that scientists research with lively interviews and irreverent commentary. You can find her twitter at @MoKrobial.

Scott Chimileski, PhD, is a microbiologist, educator, science photographer, author, and public speaker currently based at Paul Smith’s College of the Adirondacks, with ongoing affiliations at Harvard University. From 2015 to 2019, he was a postdoctoral fellow in the Kolter Lab at Harvard Medical School. Since August of 2019, he has been an Assistant Professor of Microbiology at Paul Smith’s College near Saranac Lake, NY, within the Department of Natural Sciences.