Risk assessment for isolating and working with the microbial colours around us
If we’re covered in microbes why might there be a risk in growing them?
Microbes exist all around us: on almost every surface, in the air, on food, and in our bodies. Even when it seems like we are alone there are millions of organisms living their lives alongside us. This diversity and ubiquity is part of what motivated us to do this project: there are hidden colours all around us. Typically, microbes that find their way into our bodies contend with our immune system and pose no risk to our health. However, pathogenic organisms have specific strategies to circumvent or overcome our immune systems and consequently have the capacity to cause disease. These pathogens typically only grow in large numbers in their hosts, so the population in the environment is usually very low (Li, et al 2024) We do not want to use potential pathogens as pigments in the BioArtBot.
The number of microbes is also a factor in whether or not there is any risk to our health. There are small amounts of many different types of microbes scattered about in our daily lives, and they typically do not impact our health negatively. However in the BioArtBot project, we grow microbes in larger numbers in order to see their colour and paint with them. We must also grow in these larger numbers when we are looking for new pigmented microbes. With this growth comes an increased exposure to microbes and, with increased exposure comes an increased risk. It’s important that we understand this risk so that we keep ourselves and others safe.
Thinking through potential hazards and reducing risk
The process of thinking through what we are going to do and coming up with a plan to do it safely is called a risk assessment. It is used by labs to evaluate the risks present in working with the materials and methods required to get the project done and so we should do one of these too (Biosecurity & health security protection 2020)
To recap, although there are microbes everywhere, they’re typically in low numbers and not adapted against our immune system. This means on a day-to-day basis we don’t experience a great health risk from the microbes around us. But in this project we’ll be growing them to amounts higher than what you might typically encounter outside of the lab. Importantly, we don’t know exactly what microbes are present in the samples. The commonly accepted approach when working with unknown microbes from the environment is to treat them like potential pathogens that pose a moderate individual risk and low community risk (Emmert 2013). That is to say, if we grow something from the environment then we should assume that it could cause us disease but we don’t have to go as far as assuming that it could cause an epidemic if released. Since the microbial population in our environmental sample isn’t changed by our sampling —unless there is some reason to suspect a higher risk from those samples—we don’t have to take elevated precautions before the microbes start to grow. However, once they grow we have to treat the biological material as potentially pathogenic.
We want to use agar plates to grow microbes from a variety of environmental samples that are meaningful to us and our community. This process will have us pipetting dilutions of the environmental sample onto agar plates as well as separating out the pigmented microbes we find to grow them separately. Since microbes are tiny, they can hitch a ride on or otherwise become suspended in particles known as aerosols that float in the air and can be inhaled or ingested by those in the vicinity (National research council 1989). Processes like centrifuging, opening tubes, and pipetting create aerosols, so we will inevitably be creating aerosols during the course of our project. Therefore we need facilities that mitigate the risk of working with aerosols as shown in the image below (Who headquarters 2004).
Biosafety levels stipulate what personal protections and lab facilities should be used to reduce the risk of injury for those that work with organisms. At biosafety level 2 (BSL2) the risk of aerosols when cultivating organisms are mitigated by using specific equipment and having the workspace separated from other spaces (National research council 1989). Some teaching labs are BSL2 because certain interesting activities can only be performed with potential pathogens. We will also have to work in such a lab if we are going to handle the organisms after we grow them. However, as we mentioned earlier we don’t want to use potential pathogens as pigments for the BioArtBot so we will also need an approach to identify pigmented microbes in order to work with them without the elevated measures of BSL2.
We need accurate microbial identification to finalize our palette selection
In our second lab note, we proposed several pigmented organisms previously described by other labs as candidates for our San Francisco-based palette. These organisms do not require BSL2 practices and instead can be handled at a lower level called biosafety level 1 (BSL1). Many community labs are BSL1 because it is the least complex to establish. Since we want our place-based palettes to be widely used, we only want organisms that can be worked on in BSL1 conditions and thus we need to identify the organisms we isolate before they can be incorporated in the BioArtBot palette.
Microbial identification requires matching genotypic and/or phenotypic characteristics of the microbe in question to a reference microbe (United states pharmacopeia 2011) These analytical approaches come with their own limitations so confirming using multiple approaches would be the most robust. Colour is a phenotypic characteristic and can easily be assessed along with colony morphology when isolating colonies on spread plates or from a streak. Furthermore, the choice of media and environmental sample narrows the possible microbes it could be. Coupling these observations with a 16S sequence—a genotypic marker—should allow us to confidently identify a microbe cultivated from environmental samples.
Once we are confident that we’ve identified the kind of microbe we have - and that it’s not pathogenic - we can add it to our place-based palette. With enough colours in our palette, we’ll make microbial art that is ecologically connected to our environment.
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