Low-retention swabs have been developed to isolate minute amounts of biological material for subsequent analysis for surface sampling; however, these swab-based techniques are currently incompatible with quantitative approaches, due to interpersonal variation in the strength of swabbing.Commonly used active air sampling methods include liquid impingers, size-resolved and non-size-resolved impaction-based filter methods , and wetted wall cyclones. Active air samplers operate at a range of airflow rates . While the advantage of higher flow rates is that more biomass can be collected over shorter amounts of time, there remain practical size and noise concerns associated with the higher flow rate pumps. A newly developed air-sampler relies on electro-kinetic air ionization to positively charge particles in the air, and then collect them onto a negatively charged surface. Commonly used passive air sampling methods include Petri dishes suspended in air, both with and without a growth medium, dust fall collector, and sampling of portions of used HVAC filters from recirculating air handling units. A few studies have compared the ability of various bioaerosol samplers to deliver repeatable results using molecular analysis techniques or for various analysis techniques to deliver repeatable microbial community results from a particular air sampling method. Airborne collection methods can vary widely in their collection efficiencies for different sizes of bioaerosols, as well as in their DNA extraction efficiencies from the sample collection media. One recent study suggests that because different air sampling methods can yield such different results,marijuana growing equipment it may be more appropriate to use a variety of techniques to provide a more complete representation of microbial communities present indoors, consistent with recommendations before next-generation DNA sequencing.

Overall, particle collection techniques involve difficult trade-offs between ease of use, cost, and unobtrusiveness with the amount of biomass collected, the impact of the collection on viability, and the consistency and representativeness of the targeted sample.Once particles have been collected, analysis techniques are structured toward providing physical , chemical , or biological attributes. See Q5 for a discussion of current biological techniques.Online methods are emerging that provide high time-resolution and are easy to use, such as those based on laser-induced fluorescence , chemical marker detection, or other techniques, but specificity is currently limited. In spite of this limitation, LIF-based particle counting is a useful choice in studies where the study of dynamic processes is of interest, or where information on particle size is critical. In studies where processes of interest have longer timescales, or if the schedule of particle collection can be dynamically managed to target conditions of interest, particle collection/ analysis offers greater specificity to well-defined outcomes.Aside from the specific method of sampling, there are additional questions of where in a building to sample and how many areas need to be studied to give a spatially and temporally representative outcome. For spatial resolution, current research indicates that areas that vary in their degree and nature of human contact and water exposure exhibit greater compositional differences than those accumulating environmental microbes in other way.Temporal variability of microbes indoors can be high, varying on the order of hours for air samples are likely due in part to diurnal activity of outdoor microbes and to activity levels in the room and, of course, across longer time scales of weeks, months, and seasons. It has been suggested previously that sampling on different days is necessary to obtain a representative sample of aerosol exposure in a home  and that sampling time on the order of 5e7 days better captures ergosterol concentrations in homes than <24 h air samples due to the considerable temporal variability in bioaerosols.

Since repeated or long-term sampling is not always practical, especially in larger epidemiological studies, settled dust is often used as a surrogate. While it is unclear precisely what portion of exposure originates from floor dust, it is likely to be high, given the strong role that resuspension plays on structuring bioaerosols.There are many opportunities for technological improvements in the way built environments are studied and sampled. Many of these have to do with bridging biological-oriented sampling, particularly those relying on genetic assays, with particle-based sampling. One major area in need of improvement is how microbes are collected from air for later biological processing. Ideally, samplers would be easy to operate and the sampling protocol would permit consistent use with little to no formal training. This would also allow indoor sampling to be scalable, and enable the sampling of homes or other buildings across the globe that differ in design and operation with minimal cost and logistical hurdles. When using DNA sequencing approaches to survey bioaerosols in buildings, it is critical that the sampling strategy yields sufficient amounts of retrievable DNA for downstream analyses. Current approaches overcome this by taking time-integrated samples, typically over many hours. Time-integrated samples capture a composite view of bioaerosols, which can vary substantially over time. At the same time, time-resolved methods would provide repeated samples continuously over a representative period of time to link specific activities and conditions with the effects on aerosols, as is commonly done with particles. Ideally, the time-resolved methods would also provide information on particle size, which would allow the application of pre-existing understanding of aerosol behavior to better predict and control the dynamics of microorganisms in the built environment. The ideal aerosol sampler would also provide quantitative and reproducible estimates of the amounts and types of bioaerosols found within buildings. Additional technological developments and availability of low cost built-environment sensors will enable the appropriate “metadata” to be acquired more easily along with microbiological measurements, to link microbial findings to underlying causes.

Spatial mapping , advanced visualization, and other emerging tools will enable the more effective and creative application of the data made available through current molecular and building measurement technologies. Lastly, other areas of technological improvements are related to microbiological analytical methods. Efforts should be extended broadly to include eukaryotes beyond fungi, and also viruses. Approaches are necessary to address the multiple sources of bias that may be present in next-generation sequencing based characterization of microbial communities, including DNA extraction methods, primer bias, and variable gene counts and genome sizes . Improved bio-informatic approaches and reference databases will enhance our ability to study the entire microbial community. Improved and validated approaches for discriminating between dead microbes and those that are alive, and particularly methods that are compatible with current genetic-based microbial detection,greenhouse rolling benches would greatly improve our understanding of microbes in buildings. Dead pathogens inside homes and buildings may be of little concern, although allergenic fungal species may still contain allergens regardless of viability. DNA can be remarkably persistent on surfaces and particles. Plus, analytical standards for microbial community analyses would facilitate testing different molecular approaches and comparing results obtained using different strategies . Lastly, new tools for studying microbial activity in situ would provide a basis to better understand what are the primary microbial processes and in real-world buildings. While many tools focus on DNA, we also need continued advances in metatranscriptomics and metaproteomics to make these techniques more accessible.There is a growing appreciation of the impact that micro-biomes have on the health of humans. Humans can acquire some components of their own micro-biome from their surroundings and are continuously exposed to the indoor micro-biome, so it follows that the micro-biomes found in the indoor environment could also have a profound effect on human health. Recent research has highlighted this potential connection between the indoor micro-biome and health, although many of the recently published connections thus far are based on correlation, not causation. The indoor micro-biome could influence health through inhalation, ingestion, and dermal contact, and there are numerous examples of a direct link between specific microbes in the indoor environment and acute infections. Indoor air can serve as a transmission route for pathogens including Mycobacterium tuberculosis, influenza, and the fungus Aspergillus. One of the most common hospital acquired infections in the United States is caused by the bacterium Clostridium difficile, and can lead to lethal diarrhea. C. difficile forms spores that can survive on indoor surfaces, even after the use of antimicrobial products. HAIs derived from Staphylococcus aureus and the antibiotic resistant strains such as methicillin-resistant S. aureus also frequently contaminate environmental surfaces.

Water can also serve as a source of infection transmission in the built environment. A widely recognized infectious bacterium that thrives in warm water and can become aerosolized is Legionella.While it is well known that building cooling towers can contribute to the spread of Legionnaire’s disease , other building operational parameters can also influence the transmission of infectious disease. Understanding the link between the micro-biome of the indoor environment and non-infectious diseases, such as respiratory ailments, is an active area of research. There is still much work to be done to appreciate the connections between microbial diversity, environmental exposure, and health outcomes across buildings in a variety of settings, especially because for many of the associations the specific causative agents remain unknown. Early on, there were investigations into sick building syndrome , a syndrome in which occupants experience acute health symptoms while in the building including fatigue, headaches, and irritation in the eyes, nose, and throat. In a similar vein, dampness and mold in buildings are known to be detrimental for respiratory-based diseases, particularly exacerbation of existing asthma. It is logical to consider that the ill effects derive from exposure to the microbial agents endogenously growing in these water damaged buildings, but lower fungal diversity has been shown to be predictive of asthma development. In fact, Dannemiller et al., using next-generation sequencing of fungal DNA, found that no individual fungal taxon was associated with asthma development but overall fungal diversity was. On the other hand, Ege et al., working in farm environments, found that a diverse microbial environment and the presence of bacteria from particular genera were inversely associated with asthma, atopic sensitization, and hay fever. Similarly, Lynch et al. carried out a longitudinal study in inner-city environments and found that children exposed to specific types of bacteria in combination with well-known allergens at high levels had a reduced risk of allergic disease. The authors suggested that mice and cockroaches were the sources of these bacteria associated with a beneficial health outcome. In addition, even dead cells and cell fragments can have negative health impacts on respiratory health, and microbial metabolites may also directly affect human health. Clearly, there is much to learn about the interplay between overall microbial diversity and composition, the presence of particular taxa, and the built environment, and the overall effect of this milieu on immune function. In what may be the only study showing a direct health benefit from an indoor microbe, Fujimura et al. showed that exposure to dog-associated bacteria from house dust in a mouse model was protective against airway allergen challenge. Moreover, the researchers isolated a single species associated with the dog associated house dust, Lactobacillus johnsonii, and found that intentional supplement with this bacterial species conferred airway protection in mice. In addition to the inhalation and ingestion routes of environmental exposure, direct contact between surfaces and an occupant could alter the skin micro-biome. While the skin micro-biome of diseased states is distinct from that of a healthy individual with some ailments, it is unclear whether this arises through contact with the built environment and whether the skin micro-biome influences the body’s larger immune system.Decisions that are made during building design have the potential to drive the indoor micro-biome regardless of their intention or motivation. As a sterile indoor environment is not possible, nor likely to be desirable , it has been suggested to move from treating all microorganisms as contaminants towards a more bio-informed design that considers impacts of the micro-biome in design decisions. However, it is not currently clear what constitutes a healthy indoor micro-biome, nor what are the necessary design parameters to drive the micro-biome to a healthy micro-biome. With regards to infrastructure health and maintenance, plumbing systems have received the most research attention. Altering the operation of a drinking water system, for example reducing flow and moving towards green building design or using onsite drinking water disinfection, has previously been shown to alter both the micro-biome as well as potential pathogens.