Biosecurity efforts are built around the high probability of future pandemic-level pathogens. 

Many highly effective transmission interventions act on microbial environments broadly— such as indoor air and surfaces — and are not highly selective for specific pathogens. When we don't know what will make us sick, this sounds like a good bet.

But a pathogen is a microbe in a context where it causes disease. In many cases, the difference between a harmless and a pathogenic microbe is context. Most microbes we encounter don't cause us harm, and many play important roles in long-term human health and development from birth. 

In this piece I outline this context and highlight the need for biosecurity interventions that are more selective — reducing harmful microbial exposure while preserving beneficial microbial exposure.

I'm by no means a field-level expert here so would really value discussion and ideas -- I've included a few questions to wrap-up.

Context: 

• Emerging research about the human microbiome suggests our bodies are home to trillions of microbes including viruses, bacteria and fungi.
• Our microbial communities — our microbiome — live on and in our bodies, comprising an ecosystem of species that can have beneficial symbiotic effects, neutral effects, and, of course, pathogenic effects. 
• Some microbes drive critical aspects of health and development, such as immune system development and response (including inflammation), digestion and metabolism, and brain development and mood. 
• Reduced or altered microbiomes have been associated with increased risk of several chronic conditions such as allergies, metabolic disorders, and inflammatory disease. The magnitude and mechanisms of these effects remain uncertain.
• These microbes come from the world around us from the moment of birth throughout life, shaped by where we live, work and play, what we eat, how we medicate, who we encounter, etc. In modern, industrialized settings, people spend up to 90% of their time/life indoors. The indoors — the built environment — is a major source of and influence on our microbiome.
• Biosecurity is expressly focused on real or potential pathogens that could pose a serious threat to our health at the population-level, society-level, and even species-level. Robust, feasible and resourced pandemic-level pathogen prevention and response plans are critical to our safety and security. 
• Preventing and reducing pathogen transmission is a central pillar of this work.
• The recent COVID19 pandemic increased attention to indoor pathogen transmission and highlighted the risks associated with indoor spaces.
• Biosecurity efforts have prioritized indoor spaces as a target for transmission reduction and prevention, focusing on physical barriers like PPE, surface sterilization, and air ventilation and purification. 
• Some existing and proposed interventions preserve microbial diversity better than others, but this distinction is rarely foregrounded in biosecurity design.
• Given the important ways indoor spaces contribute to the human microbiome and, through this, our long-term health and development, it seems important to consider how biosecurity efforts to reduce and prevent pathogen transmission affect microbial diversity.

Problem: 

• Current biosecurity frameworks largely optimize for pathogen reduction without explicitly accounting for the need to maintain beneficial microbial exposure.
• The result is interventions designed to control pathogen transmission and prevent infectious disease through broad, non-selective microbial exposure reduction that may reduce beneficial microbial exposures with potential long-term health implications, given links between microbiome disruption and chronic conditions.
• This has parallels to the unintended and underrecognized microbiome impacts seen with using broad-spectrum antibiotics as a means to target one pathogen.

Need:

• We need pathogen-control interventions designed and evaluated not only for infection reduction but also for their effects on beneficial environmental microbial exposure.
• The need is for designing interventions that are more selective in what they remove, not at the expense of weakening infection control.

Urgency:

• We are in a window of opportunity in biosecurity: standards for indoor air safety, pandemic preparedness infrastructure, and resilient building design are actively being developed now. This is a field currently under construction — field-building, priority-setting, and intervention development are all under way and can be influenced to address the need.

Opportunity:

• We can achieve this through intentional field-building, integrating microbiome and built environment evidence and perspectives into biosecurity intervention design and evaluation.
• Examples: Advisory roles for microbiome and built environment experts on biosecurity projects and teams; Convening diverse agenda-setting networks; Design challenges or funding calls for microbiome-informed approaches.

Questions worth discussing & exploring:

• Which biosecurity interventions are most likely to reduce beneficial microbial exposure in practice?
• Are there existing approaches that successfully balance pathogen control and microbial diversity?
• What evidence would be most valuable to evaluate this tradeoff?