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4 Tools for Characterizing MicrobiomeBuilt Environment Interactions
Pages 147-188

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From page 147...
... • Approaches for characterizing the microbial communities in built environments include direct culturing, use of a variety of "omics" techniques, and other molecular measurements; the goal is to identify microorganisms and characterize their functional activities. • Key tool and infrastructure gaps include furthering agreement on sampling and on the building and occupant data to collect in parallel with microbial samples; developing reference mate­ rials, standards, and assessment approaches; and improving the ability to share and access data effectively and to compare results across studies.
From page 148...
... Topics discussed include standardized methods for collecting data on built environments and microbial communities and tools for analyzing these data to improve understanding of microbiome–built environment interactions. The chapter considers a number of factors important to characterizing buildings and microbial communities.
From page 149...
... Sources That Populate Indoor Microbial Communities As discussed in Chapter 3, the microbial communities within built environments derive from a mix of outdoor microorganisms brought indoors through air, water, and occupants and microorganisms from indoor sources. Indoor microbial communities also include microorganisms shed from those who occupy the building, and they are influenced by microbial growth and death driven by indoor environmental conditions, such as the availability of moisture.
From page 150...
... The data collection effort undertaken for the Hospital Microbiome Project illustrates how such measurements can be implemented. This project explored the composition of microbial communities in 10 patient rooms and two nursing stations on two floors of a newly constructed hospital before and after occupancy by patients (Lax et al., 2017; Ramos et al., 2015; Shogan et al., 2013; Smith et al., 2013)
From page 151...
... . Collaborative consortia -- such as SinBerBEST, ­ which involves the University of California, Berkeley; Nanyang Technological University; and the National University of Singapore -- are also working to develop and improve building sensors to support efficiency, sustainability, and indoor air quality.1 The three areas highlighted below represent 1  See http://sinberbest.berkeley.edu (accessed May 11, 2017)
From page 152...
... Measuring Ventilation Type and Airflow Rate As emphasized in Chapter 3, buildings vary greatly in design and operation, including in the HVAC systems they employ and how these systems are operated, the extent and timing of outdoor air intake versus indoor air recirculation, the ventilation rates, the use and efficiency of air filtration, and other measures. In the context of built environment–microbiome s ­tudies, there is no typical building, and one cannot assume ventilation and airflow parameters based only on building type.
From page 153...
... Once researchers have a map of the dynamic flux of microbes between individuals and the built environments they occupy, it is possible to start asking questions about how such a flux could influence health outcomes for occupants. In addition to tracking pathogen exposure and transmission, it is also possible to explore the broader microbial exposure an individual patient receives, either at home, in a hospital, or in a work setting.
From page 154...
... Measuring Occupancy and Human Activities The role of humans and human activities in the built environment is complex and combines with building characteristics to affect microbial communities. The density of occupants in the environment affects not 2  The dynamics of particles settling from air is dependent on such factors as the particles' aerodynamic diameter, which takes into account the effects of density.
From page 155...
... Building Simulation Tools A number of design and analysis simulation tools can be useful in understanding the factors impacting environmental conditions that are potentially conducive or unfavorable to indoor microbial growth. Design tools are those used specifically to support building design, while analysis tools are also used to study building performance issues that are not necessarily part of the design process -- for example, trying to understand indoor air quality problems in an existing building or to analyze experimental data.
From page 156...
... nant transport, and moisture conditions.3 An important task for future work will be to couple such simulation models for the built environment with explicit population dynamics models (alluded to in Box 1-2 in Chapter 1) for diverse, complex microbial communities.
From page 157...
... . CHARACTERIZING INDOOR MICROBIAL COMMUNITIES In addition to information about building design and operations, s ­tudies aimed at understanding the impacts of microbial communities in built environments rely on tools that characterize these microbiomes and their functional activities.
From page 158...
... For example, many studies aimed at characterizing indoor microbial communities employ analyses of microbial nucleic acids. However, recovering microbial DNA or RNA for quantitative analysis depends not only on the sampling method(s)
From page 159...
... must be included with the cohorts of indoor environment samples when genetic observations are the goal. Sample handling and preservation can have a significant effect on the subsequent analysis of genetic material recovered from environmental samples, regardless of microbial origins (viral, fungal, or bacterial)
From page 160...
... In addition, they need to be able to identify the absence of a particular target when it is not present in the sample. For example, if DNA is extracted from an air filter that also contains pollen particles, a large portion of the recovered genomic material may yield plant genomes rather than the target genomes of the indoor microbial communities (Be et al., 2015)
From page 161...
... Some functional markers may be able to provide a finer level of taxonomic resolution than common phylogenetic markers, however. All tools have strengths and limitations with regard to balancing sensitivity, specificity, organism coverage, and taxonomic resolution.
From page 162...
... All measurements are made in comparison with standards, and defining and developing appropriate, validated standards for measurement of microbial communities remains an issue for microbiome studies. Even were such standards available, it is difficult to provide quantitative information with amplicon sequencing and shotgun sequencing approaches (Nayfach et al., 2016; Zhou et al., 2011)
From page 163...
... Culture-based measures thus are limited as to the information about microbial communities they can provide. Crucially, researchers also need to know what the microorganisms in a built environment are doing.
From page 164...
... Understanding the functional activities of microorganisms in microbial communities in a built environment remains a particular challenge. Because the functions asso­ ciated with particular genes and molecules may remain unknown, even recovery of the complete complement of proteins, genes, or metabolites does not automatically yield an accurate functional assessment.
From page 165...
... . To help address reproducibility and cross-experiment comparison, several benchmarking efforts and efforts to develop reference microbial communities have been and continue to be undertaken.
From page 166...
... Developing a better understanding of the conditions under which accurate and reproducible microbiome measurements in built environments can be made will be a foundational requirement for moving investigative research in this area toward practical applications. LINKING ANALYSIS OF MICROBIAL COMMUNITIES TO BUILDING CHARACTERISTICS AND HUMAN HEALTH IMPACTS Gaining a holistic picture of how the design and operations of built environments, the identities and functions of microbial communities, and potential impacts on humans and the environment are interconnected will require new studies and study designs, particularly as research moves beyond ecological characterization and toward translation and application.
From page 167...
... • Identify features of the built environment hypothesized to be rel evant through their effects on indoor microbial communities or their direct impacts on human health. Identify strategies and techniques for measuring these features of the built environment.
From page 168...
... Given the multitude of factors influencing microbial communities in buildings and human exposures to those communities and the difficulties of trying to disentangle effects on health, intervention studies can be useful in further testing relation ships hypothesized or observed through observational studies and in animal models.
From page 169...
... Applying epidemiologic and animal studies to understand exposure to a specific microorganism, such as a pathogen, is more straightforward than applying such studies to tease out multiple microbial exposures, such as those that occur in ­ most built ­ nvironments. For example, to understand how characteristics e of the built environment and its microbiome influence childhood neuro­ development and neurocognitive outcomes, it will be essential to consider the sample types that should be collected and the microbial parameters that should be measured to characterize the relevant exposures.
From page 170...
... For microbiome analysis, a sample needs to have been handled and stored appropriately, and its utility can be assessed qualitatively based on the expectation for microbial profiles associated with similar built environments. Having a high-quality sample may not be absolutely necessary if the degradation of the community signature was not so complete that it impaired the ability to detect trend differences among different conditions.
From page 171...
... Acute events such as Hurricanes Katrina and Sandy resulted in widespread flooding of homes and underground subway stations, and they provided an opportunity to examine how microbial communities changed when exposed to these extreme conditions.
From page 172...
... The ability to compare results across studies enables researchers to better assess converging lines of independent evidence in parsing the factors that affect the formation and functions of microbial communities in built environments. Efforts to generate standards for the collection of data and metadata, common storage formats and resources, and microbial reference materials that can be used to calibrate results across laboratories are important in addressing this need.
From page 173...
... Also important is requiring that the software tools and detailed scientific workflows used to generate an analysis be made available for peer review to help ensure that results are independently verifiable. Supporting Sharing of Data on Microbial Communities and Metadata on Buildings and Building Systems Through the Use of Data Commons A data commons is a collection of computational resources that provide a common platform for access to data sources for analysis, supporting a community of researchers.
From page 174...
... Moreover, microbiome–built environment data are collected from a diverse array of research efforts across multiple institutions and research disciplines, all with the need for analysis tools that can operate on these data collections using a potentially distributed set of computing resources to support scalable and independent analysis, and in ways that enable individual investigators to contribute to the field as a whole. A data commons can also provide access to common analytic pipelines, the contents, logic, and algorithms of which are public and that provide standards for analysis, such as in community profiling.12 A previous effort to develop minimum requirements for building metadata led to a defined set of data to be collected in conjunction with experimental studies of indoor microbial communities -- the MIxS-BE package.
From page 175...
... Given that the BASE protocol was developed more than 20 years ago, it may be useful to update it for its potential application to indoor microbial studies and to continue efforts to develop common data templates. The trade-offs between obtaining as much useful information as possible to characterize buildings, occupants, and their environments and the volume of information to be collected and analyzed also will require further discussion and agreement.
From page 176...
... • Best practices for building design and operation can be described in reports and other documents written by researchers and other experts and intended for practitioners. • Voluntary guidance on how to design and operate buildings to sup port improved indoor microbial environments can be produced by engineering and professional societies, such as the American Indus trial Hygiene Association (AIHA)
From page 177...
... In practice, these minimum values are used without considering the potential benefits of higher levels of outdoor air intake. It is important to bear in mind that while ventilation requirements are important for establishing building design goals, they are only a first step in the process of achieving effective ventilation in buildings.
From page 178...
... Communicating to people that they are surrounded by microbial communities whose effects may include beneficial, neutral, or harmful interactions and providing people with information they need to make choices about their built environments are important goals. At the same time, investigators will want to avoid promoting unjustified fears about the microbial ecosystems that coexist with humans or overselling the strength of available evidence.
From page 179...
... The research infrastructure that supports the field includes components that affect the ability of investigators to collect, analyze, store, share, and compare information. Important aspects of this system include continued improvements in microbial and building characterization tools, data collection standards, reference materials, and benchmarking efforts, such as the devel­ opment of mock microbial communities, validation of experimental approaches, and resources for accessible data storage and sharing to facilitate cross-study comparison and the generation of new hypotheses.
From page 180...
... A framework for establishing further infrastructure to support this field will usefully include the devel­ opment of shared understandings among investigators on sample and metadata collection and on sample handling, storage, and pro cessing conditions to support effectively addressing different types of research questions, along with the promulgation of best practices and metrics for analysis. The research infrastructure will need to encompass the use of a variety of complementary experimental, modeling, and analysis tools to understand the composition and function of microbial communities and to connect such research to
From page 181...
... 2. Develop infrastructures and practices to support effective communi cation and engagement with those who own, operate, occupy, and manage built environments.
From page 182...
... 2009. Diffusive sam pling and measurement of microbial volatile organic compounds in indoor air.
From page 183...
... 2012. Low sequencing efforts bias analyses of shared taxa in microbial communities.
From page 184...
... Indoor Air 22(4)
From page 185...
... 2004. Detection of genes involved in biodegradation and biotransformation in microbial communities by u ­ sing 50-mer oligonucleotide microarrays.
From page 186...
... 2013. A metagenomics framework for the study of airborne microbial communities.
From page 187...
... CHARACTERIZING MICROBIOME–BUILT ENVIRONMENT INTERACTIONS 187 Zou, H., Z


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