Microbes and associated soluble and volatile chemicals on periodically wet household surfaces

Biocontrol in built environments to reduce pathogen exposure and infection risk

The microbiome of the built environment comprises bacterial, archaeal, fungal, and viral communities associated with human-made structures. Even though most of these microbes are benign, antibiotic-resistant pathogens can colonize and emerge indoors, creating infection risk through surface transmission or inhalation. Several studies have catalogued the microbial composition and ecology in different built environment types. These have informed in vitro studies that seek to replicate the physicochemical features that promote pathogenic survival and transmission, ultimately facilitating the development and validation of intervention techniques used to reduce pathogen accumulation. Such interventions include using Bacillus-based cleaning products on surfaces or integrating bacilli into printable materials. Though this work is in its infancy, early research suggests the potential to use microbial biocontrol to reduce hospital- and home-acquired multidrug-resistant infections. Although these techniques hold promise, there is an urgent need to better understand the microbial ecology of built environments and to determine how these biocontrol solutions alter species interactions. This review covers our current understanding of microbial ecology of the built environment and proposes strategies to translate that knowledge into effective biocontrol of antibiotic-resistant pathogens.

RNA-based amplicon sequencing is ineffective in measuring metabolic activity in environmental microbial communities

BACKGROUND

Characterization of microbial activity is essential to the understanding of the basic biology of microbial communities, as the function of a microbiome is defined by its biochemically active ("viable") community members. Current sequence-based technologies can rarely differentiate microbial activity, due to their inability to distinguish live and dead sourced DNA. As a result, our understanding of microbial community structures and the potential mechanisms of transmission between humans and our surrounding environments remains incomplete. As a potential solution, 16S rRNA transcript-based amplicon sequencing (16S-RNA-seq) has been proposed as a reliable methodology to characterize the active components of a microbiome, but its efficacy has not been evaluated systematically. Here, we present our work to benchmark RNA-based amplicon sequencing for activity assessment in synthetic and environmentally sourced microbial communities.

RESULTS

In synthetic mixtures of living and heat-killed Escherichia coli and Streptococcus sanguinis, 16S-RNA-seq successfully reconstructed the active compositions of the communities. However, in the realistic environmental samples, no significant compositional differences were observed in RNA ("actively transcribed - active") vs. DNA ("whole" communities) spiked with E. coli controls, suggesting that this methodology is not appropriate for activity assessment in complex communities. The results were slightly different when validated in environmental samples of similar origins (i.e., from Boston subway systems), where samples were differentiated both by environment type as well as by library type, though compositional dissimilarities between DNA and RNA samples remained low (Bray-Curtis distance median: 0.34-0.49). To improve the interpretation of 16S-RNA-seq results, we compared our results with previous studies and found that 16S-RNA-seq suggests taxon-wise viability trends (i.e., specific taxa are universally more or less likely to be viable compared to others) in samples of similar origins.

CONCLUSIONS

This study provides a comprehensive evaluation of 16S-RNA-seq for viability assessment in synthetic and complex microbial communities. The results found that while 16S-RNA-seq was able to semi-quantify microbial viability in relatively simple communities, it only suggests a taxon-dependent "relative" viability in realistic communities.  Video Abstract.

Volatile Organic Compound (VOC) Profiles of Different Trichoderma Species and Their Potential Application

Fungi emit a broad spectrum of volatile organic compounds (VOCs), sometimes producing species-specific volatile profiles. Volatilomes have received over the last decade increasing attention in ecological, environmental and agricultural studies due to their potential to be used in the biocontrol of plant pathogens and pests and as plant growth-promoting factors. In the present study, we characterised and compared the volatilomes from four different Trichoderma species: T. asperellum B6; T. atroviride P1; T. afroharzianum T22; and T. longibrachiatum MK1. VOCs were collected from each strain grown both on PDA and in soil and analysed using proton transfer reaction quadrupole interface time-of-flight mass spectrometry (PTR-Qi-TOF-MS). Analysis of the detected volatiles highlighted a clear separation of the volatilomes of all the four species grown on PDA whereas the volatilomes of the soil-grown fungi could be only partially separated. Moreover, a limited number of species-specific peaks were found and putatively identified. In particular, each of the four Trichoderma species over-emitted somevolatiles involved in resistance induction, promotion of plant seed germination and seedling development and antimicrobial activity, as 2-pentyl-furan, 6PP, acetophenone and p-cymene by T. asperellum B6, T. atroviride P1, T. afroharzianum T22 and T. longibrachiatum MK1, respectively. Their potential role in interspecific interactions from the perspective of biological control is briefly discussed.

Henry's Law Constants and Indoor Partitioning of Microbial Volatile Organic Compounds

Microbial volatile organic compounds (MVOCs) play an essential role in many environmental fields, such as indoor air quality. Long-term exposure to odorous and toxic MVOCs can negatively affect the health of occupants. Recently, the involvement of surface reservoirs in indoor chemistry has been realized, which signifies the importance of the phase partitioning of volatile organic pollutants. However, reliable partition coefficients of many MVOCs are currently lacking. Equilibrium partition coefficients, such as Henry's law constant, H, are crucial for understanding the environmental behavior of chemicals. This study aims to experimentally determine the H values and their temperature dependence for key MVOCs under temperature relevant to the indoor environment. The H values were determined with the inert gas-stripping (IGS) method and variable phase ratio headspace (VPR-HS) technique. A two-dimensional partitioning model was applied to predict the indoor phase distribution of MVOCs and potential exposure pathways to the residences. The findings show that the MVOCs are likely distributed between the gas and weakly polar (e.g., organic-rich) reservoirs indoors. Temperature and the volume of reservoirs can sensitively affect indoor partitioning. Our results give a more comprehensive view of indoor chemical partitioning and exposure.

The sanitary indoor environment-a potential source for intact human-associated anaerobes

A healthy human microbiome relies on the interaction with and exchange of microbes that takes place between the human body and its environment. People in high-income countries spend most of their time indoors and for this reason, the built environment (BE) might represent a potent source of commensal microbes. Anaerobic microbes are of particular interest, as researchers have not yet sufficiently clarified how the human microbiome acquires oxygen-sensitive microbes. We sampled the bathrooms in ten households and used propidium monoazide (PMA) to assess the viability of the collected prokaryotes. We compared the microbiome profiles based on 16S rRNA gene sequencing and confirmed our results by genetic and cultivation-based analyses. Quantitative and qualitative analysis revealed that most of the microbial taxa in the BE samples are human-associated. Less than 25% of the prokaryotic signatures originate from intact cells, indicating that aerobic and stress resistant taxa display an apparent survival advantage. However, we also confirmed the presence of intact, strictly anaerobic taxa on bathroom floors, including methanogenic archaea. As methanogens are regarded as highly sensitive to aerobic conditions, oxygen-tolerance experiments were performed with human-associated isolates to validate their survival. These results show that human-associated methanogens can survive oxic conditions for at least 6 h. We collected strong evidence that supports the hypothesis that obligate anaerobic taxa can survive in the BE for a limited amount of time. This suggests that the BE serves as a potential source of anaerobic human commensals.

Diversity and Metabolic Activity of Fungi Causing Biodeterioration of Canvas Paintings

Research into the biodeteriorative potential of fungi can serve as an indicator of the condition of heritage items. Biodeterioration of canvas paintings as a result of fungal metabolic activity is understudied with respect to both the species diversity and mechanisms involved. This study brings new evidence for the physiology of fungi biodeteriorative capacity of canvas paintings. Twenty-one fungal isolates were recovered from four oil paintings (The Art Museum, Cluj-Napoca) and one gouache painting (private collection), dating from the 18th to 20th centuries. The species, identified based on the molecular markers Internal Transcribed Spacer (ITS), beta-tubulin (tub2), or translation elongation factor 1 (TEF-1), are common colonisers of canvas paintings or indoor environments (e.g., Penicillium spp., Aspergillus spp., Alternaria spp.). Fungi enzymatic profiles were investigated by means of hydrolysable substrates, included in culture media or in test strips, containing components commonly used in canvas paintings. The pigment solubilisation capacity was assessed in culture media for the primary pigments and studied in relation to the organic acid secretion. Caseinases, amylases, gelatinases, acid phosphatase, N-acetyl-β-glucosaminidase, naphthol-AS-BI-phosphohydrolase, and β-glucosidase were found to be the enzymes most likely involved in the processes of substrate colonisation and breakdown of its components. Aureobasidium genus was found to hold the strongest biodeteriorative potential, followed by Cladosporium, Penicillium, Trichoderma, and Aspergillus. Blue pigment solubilisation was detected, occurring as a result of organic acids secretion. Distinct clusters were delineated considering the metabolic activities detected, indicating that fungi specialise in utilisation of certain types of substrates. It was found that both aged and modern artworks are at risk of fungal biodeterioration, due to the enzymatic activities’ diversity and intensity, pigment solubilisation capacity or pigment secretion.

A modular mechanistic framework for estimating exposure to SVOCs: Next steps for modeling emission and partitioning of plasticizers and PFAS

Estimates of human exposure to semi-volatile organic compounds (SVOCs) such as phthalates, phthalate alternatives, and some per- and polyfluoroalkyl substances (PFAS) are required for the risk-based evaluation of chemicals. Recently, a modular mechanistic modeling framework to rapidly predict SVOC emission and partitioning in indoor environments has been presented, in which several mechanistically consistent source emission categories (SECs) were identified. However, not all SECs have well-developed emission models. In addition, data on model parameters are missing even for frequently studied SVOCs. These knowledge gaps impede the comprehensive prediction of the fate of SVOCs indoors. In this paper, sets of high-priority phthalates, phthalate alternatives, and PFAS were identified based on chemical occurrence indoors and additional selection criteria. These high-priority chemicals served as the basis for exploring model parameter availability for existing indoor SVOC emission and partitioning models. The results reveal that additional experimental and modeling work is needed to fully understand the behavior of SVOCs indoors and to predict exposures with greater confidence and lower uncertainty. Modeling approaches to fill some of the identified gaps are proposed. The prioritized sets of chemicals and proposed new modeling approaches will help guide future research. The inclusion of polar phases in the framework will further expand its applicability and scope. IMPACT STATEMENT: This paper compiles data on high-priority chemicals commonly found indoors and information on the availability of applicable models and model parameters to predict emission, partitioning, and subsequent exposure to these chemicals. Modeling approaches for a selection of the missing SECs (source emission categories) are proposed, to illustrate the path forward. The comprehensive data set helps inform researchers, exposure assessors, and policy makers to better understand the state of the science regarding modeling of indoor exposure to semi-volatile organic compounds (SVOCs) and per- and polyfluoroalkyl substances (PFAS).

Enabling Quantitative Analysis of Surface Small Molecules for Exposomics and Behavioral Studies

Workplace chemical exposures are a major source of occupational injury. Although over half of these are skin exposures, exposomics research often focuses on chemical levels in the air or in worker biofluids such as blood and urine. Until now, one limitation has been the lack of methods to quantitatively measure surface chemical transfer. Outside the realm of harmful chemicals, the small molecules we leave behind on surfaces can also reveal important aspects of human behavior. In this study, we developed a swab-based quantitative approach to determine small molecule concentrations across common surfaces. We demonstrate its utility using one drug, cyclobenzaprine, on metal surfaces, and two human-derived metabolites, carnitine and phenylacetylglutamine, on four common surfaces: linoleum flooring, plastified laboratory workbench, metal, and Plexiglas. We observed peak areas proportional to surface analyte concentrations at 45 min and 1 week after deposition, enabling quantification of molecule abundance on workplace built environment surfaces. In contrast, this method was unsuitable for analysis of oleanolic acid, for which we did not observe a strong linear proportional relationship following swab-based recovery from surfaces. Overall, this method paves the way for future quantitative exposomics studies in analyte-specific and surface-specific frameworks.

BioMateriOME: To understand microbe-material interactions within sustainable, living architectures

BioMateriOME evolved from a prototyping process which was informed from discussions between a team of designers, architects and microbiologists, when considering constructing with biomaterials or human cohabitation with novel living materials in the built environment. The prototype has two elements (i) BioMateriOME-Public (BMP), an interactive public materials library, and (ii) BioMateriOME-eXperimental (BMX), a replicated materials library for rigorous microbiome experimentation. The prototype was installed into the OME, a unique experimental living house, in order to (1) gain insights into society's perceptions of living materials, and (2) perform a comparative analysis of indoor surface microbiome development on novel biomaterials in contrast to conventional indoor surfaces, respectively. This review summarizes the BioMateriOME prototype and its use as a tool in combining microbiology, design, architecture and social science. The use of microbiology and biological components in the fabrication of biomaterials is provided, together with an appreciation of the microbial communities common to conventional indoor surfaces, and how these communities may change in response to the implementation of living materials in our homes. Societal perceptions of microbiomes and biomaterials, are considered within the framework of healthy architecture. Finally, features of architectural design with microbes in mind are introduced, with the possibility of codifying microbial surveillance into design and construction benchmarks, standards and regulations toward healthier buildings and their occupants.

Microbial growth and volatile organic compound (VOC) emissions from carpet and drywall under elevated relative humidity conditions

BACKGROUND

Microbes can grow in indoor environments if moisture is available, and we need an improved understanding of how this growth contributes to emissions of microbial volatile organic compounds (mVOCs). The goal of this study was to measure how moisture levels, building material type, collection site, and microbial species composition impact microbial growth and emissions of mVOCs. We subjected two common building materials, drywall, and carpet, to treatments with varying moisture availability and measured microbial communities and mVOC emissions.

RESULTS

Fungal growth occurred in samples at >75% equilibrium relative humidity (ERH) for carpet with dust and >85% ERH for inoculated painted drywall. In addition to incubated relative humidity level, dust sample collection site (adonis p=0.001) and material type (drywall, carpet, adonis p=0.001) drove fungal and bacterial species composition. Increased relative humidity was associated with decreased microbial species diversity in samples of carpet with dust (adonis p= 0.005). Abundant volatile organic compounds (VOCs) that accounted for >1% emissions were likely released from building materials and the dust itself. However, certain mVOCs were associated with microbial growth from carpet with dust such as C10H16H+ (monoterpenes) and C2H6SH+ (dimethyl sulfide and ethanethiol). CO2 production from samples of carpet with dust at 95% ERH averaged 5.92 mg hr-1 kg-1, while the average for carpet without dust at 95% ERH was 2.55 mg hr-1 kg-1.

CONCLUSION

Microbial growth and mVOC emissions occur at lower relative humidity in carpet and floor dust compared to drywall, which has important implications for human exposure. Even under elevated relative humidity conditions, the VOC emissions profile is dominated by non-microbial VOCs, although potential mVOCs may dominate odor production. Video Abstract.

Contribution of Visible Surface Mold to Airborne Fungal Concentration as Assessed by Digital Image Quantification

The rapid monitoring of total fungi, including air and surface fungal profiling, is an important issue. Here, we applied air and surface sampling, combined with digital image quantification of surface mold spots, to evaluate the contribution of surface fungi to airborne fungal concentrations. Cladosporium, Penicillium, Aspergillus, and yeast often appeared in the air or on wall surfaces during sampling. The indoor/outdoor concentration ratios (I/O ratios) demonstrated that the airborne concentrations of commonly found fungal genera outdoors were higher than those indoors (median I/O ratio = 0.65–0.91), excluding those of Penicillium and yeast. Additionally, the surface density (fungal concentration/area) of individual fungi showed no significant correlation with the airborne concentration, excluding that of Geotrichum. However, if a higher surface ratio (>0.00031) of mold spots appeared in the total area of an indoor environment, then the concentrations of Aspergillus and Geotrichum in the air increased significantly. Our results demonstrated that the airborne concentration of indoor fungi is significantly correlated with the outdoor concentration. A higher density of surface fungi does not necessarily contribute to a high fungal concentration in the air. In contrast to fungal density, quantification of the surface fungal area is recommended to assess the risk of surface fungi propelling into the air.

Bacterial colonization dynamics and antibiotic resistance gene dissemination in the hospital environment after first patient occupancy: a longitudinal metagenetic study

BACKGROUND

Humans spend the bulk of their time in indoor environments. This space is shared with an indoor ecosystem of microorganisms, which are in continuous exchange with the human inhabitants. In the particular case of hospitals, the environmental microorganisms may influence patient recovery and outcome. An understanding of the bacterial community structure in the hospital environment is pivotal for the prevention of hospital-acquired infections and the dissemination of antibiotic resistance genes. In this study, we performed a longitudinal metagenetic approach in a newly opened ward at the Charité Hospital (Berlin) to characterize the dynamics of the bacterial colonization process in the hospital environment after first patient occupancy.

RESULTS

The sequencing data showed a site-specific taxonomic succession, which led to stable community structures after only a few weeks. This data was further supported by network analysis and beta-diversity metrics. Furthermore, the fast colonization process was characterized by a significant increase of the bacterial biomass and its alpha-diversity. The compositional dynamics could be linked to the exchange with the patient microbiota. Over a time course of 30 weeks, we did not detect a rise of pathogenic bacteria in the hospital environment, but a significant increase of antibiotic resistance determinants on the hospital floor.

CONCLUSIONS

The results presented in this study provide new insights into different aspects of the environmental microbiome in the clinical setting, and will help to adopt infection control strategies in hospitals and health care-related buildings. Video Abstract.

Practitioner-driven research for improving the outcomes of mold inspection and remediation

This commentary is intended to provide a research roadmap for utilizing recent chemical and molecular-biological technological advances for addressing dampness and mold in buildings. The perspective is unique in that both the mold industry practitioners and academic researchers drive the questions. Research needs were derived from a 2018 international workshop attended by practitioners, researchers and governmental representatives, where challenges and opportunities in the mold remediation and restoration field were discussed focusing on the need to develop new tools that improve building diagnosis and clearance certification for mold inspectors and remediators. Suggestions are made on how new technologies surrounding DNA-based sequence analysis for fungal and bacterial identification and real-time chemical sensor technology can be leveraged by practitioners to improve inspection and remediation. The workshop put into effect a logical progression to distill and extract practice-based implications and encourage the process of transfer of the science to practice. Goals for the workshop, and this subsequent paper, are also centered on encouraging US government-funding agencies to better position and define research on the built environment geared for end-user scientists and practitioners to better explore practical solutions to dampness and mold in indoor environments. By facilitating the workshop forum and targeting industry, field practitioners, and government agencies, a sharing of needed commonalities may be infused into future research agendas and outreach efforts.

Microbial, environmental and anthropogenic factors influencing the indoor microbiome of the built environment

A built environment is a human-made environment providing surroundings for human occupancy, activities, and settlement. It is supposed to safeguard humans from all undesirable and harmful pollutants; however, indoor concentrations of some pollutants are much greater than that of the outdoors. Bioaerosols infiltrate from the outdoors in addition to many indoor sources of bioaerosols including the use of various chemicals as well as activities like cooking, smoking, cleaning, or even normal movement. They are also associated with a number of serious health concerns. Various ecological factors associated with the generation, the persistence as well as the dispersal of these microbial components of indoor bioaerosols, are discussed in this review, that have not been considered all together till now. The factors like microbial taxa, environmental factors, and anthropogenic activities (human occupancy, activities, and impact of urbanization) are addressed in the review. Effects of both indoor environmental factors like architectural design, lighting, ventilation, temperature, humidity, indoor/outdoor ratio, particulate matter, indoor chemistry as well as outdoor environmental factors like geography, seasons, and meteorology on the microbial concentrations have been discussed. Efforts are underway to design selective pressures for microbes to create a healthy symbiotic built microbiome as the "right" indoor microbiome is a "healthy" indoor microbiome.

Human Emissions of Size-Resolved Fluorescent Aerosol Particles: Influence of Personal and Environmental Factors

Human emissions of fluorescent aerosol particles (FAPs) can influence the biological burden of indoor air. Yet, quantification of FAP emissions from human beings remains limited, along with a poor understanding of the underlying emission mechanisms. To reduce the knowledge gap, we characterized human emissions of size-segregated FAPs (1-10 μm) and total particles in a climate chamber with low-background particle levels. We probed the influence of several personal factors (clothing coverage and age) and environmental parameters (level of ozone, air temperature, and relative humidity) on particle emissions from human volunteers. A material-balance model showed that the mean emission rate ranged 5.3-16 × 10⁶ fluorescent particles per person-h (0.30-1.2 mg per person-h), with a dominant size mode within 3-5 μm. Volunteers wearing long-sleeve shirts and pants produced 40% more FAPs relative to those wearing t-shirts and shorts. Particle emissions varied across the age groups: seniors (average age 70.5 years) generated 50% fewer FAPs compared to young adults (25.0 years) and teenagers (13.8 years). While we did not observe a measurable influence of ozone (0 vs 40 ppb) on human FAP emissions, there was a strong influence of relative humidity (34 vs 62%), with FAP emissions decreasing by 30-60% at higher humidity.

Quantitative profiling of built environment bacterial and fungal communities reveals dynamic material dependent growth patterns and microbial interactions

Indoor microbial communities vary in composition and diversity depending on material type, moisture levels, and occupancy. In this study, we integrated bacterial cell counting, fungal biomass estimation, and fluorescence-assisted cell sorting (FACS) with amplicon sequencing of bacterial (16S rRNA) and fungal (ITS) communities to investigate the influence of wetting on medium density fiberboard (MDF) and gypsum wallboard. Surface samples were collected longitudinally from wetted materials maintained at high relative humidity (~95%). Bacterial and fungal growth patterns were strongly time-dependent and material-specific. Fungal growth phenotypes differed between materials: spores dominated MDF surfaces while fungi transitioned from spores to hyphae on gypsum. FACS confirmed that most of the bacterial cells were intact (viable) on both materials over the course of the study. Integrated cell count and biomass data (quantitative profiling) revealed that small changes in relative abundance often resulted from large changes in absolute abundance, while negative correlations in relative abundances were explained by rapid growth of only one group of bacteria or fungi. Comparisons of bacterial-bacterial and fungal-bacterial networks suggested a top-down control of fungi on bacterial growth, possibly via antibiotic production. In conclusion, quantitative profiling provides novel insights into microbial growth dynamics on building materials with potential implications for human health.

Influence of indoor chemistry on the emission of mVOCs from Aspergillus niger molds

People spend 80% of their time indoors exposed to poor air quality due to mold growth in humid air as well as human activities (painting, cooking, cleaning, smoking…). To better understand the impact of molds on indoor air quality, we studied the emission of microbial Volatile Organic Compounds (mVOCs) from Aspergillus niger, cultivated on malt agar extract, using a high-resolution proton transfer reaction- time of flight- mass spectrometer (PTR-TOF-MS). These emissions were studied for different cultivation time and indoor relative humidities. Our results show that the concentration of the known C₄-C₉ mVOCs tracers of the microbial activity (like 1-octen-3-ol, 3-methylfuran, 2-pentanone, dimethyl sulfide, dimethyl disulfide, nitromethane, 1,3-octadiene…) was the highest in the early stage of growth. However, these emissions decreased substantially after a cultivation time of 10-14 days and were highly affected by the relative humidity. In addition, the emissions of certain mVOCs were sensitive to indoor light, suggesting an impact of photochemistry on the relative amounts of indoor mVOCs. Based on this study, an estimation of the mVOC concentration for a standard living room was established at different air exchange rates and their indoor lifetimes toward hydroxyl radicals and ozone were also estimated. These findings give insights on possible mVOCs levels in moisture-damaged buildings for an early detection of microbial activity and new evidences about the effect of indoor light on their emission.

Sniffing fungi - phenotyping of volatile chemical diversity in Trichoderma species

Volatile organic compounds (VOCs) play vital roles in the interaction of fungi with plants and other organisms. A systematic study of the global fungal VOC profiles is still lacking, though it is a prerequisite for elucidating the mechanisms of VOC-mediated interactions. Here we present a versatile system enabling a high-throughput screening of fungal VOCs under controlled temperature. In a proof-of-principle experiment, we characterized the volatile metabolic fingerprints of four Trichoderma spp. over a 48 h growth period. The developed platform allows automated and fast detection of VOCs from up to 14 simultaneously growing fungal cultures in real time. The comprehensive analysis of fungal odors is achieved by employing proton transfer reaction-time of flight-MS and GC-MS. The data-mining strategy based on multivariate data analysis and machine learning allows the volatile metabolic fingerprints to be uncovered. Our data revealed dynamic, development-dependent and extremely species-specific VOC profiles from the biocontrol genus Trichoderma. The two mass spectrometric approaches were highly complementary to each other, together revealing a novel, dynamic view to the fungal VOC release. This analytical system could be used for VOC-based chemotyping of diverse small organisms, or more generally, for any in vivo and in vitro real-time headspace analysis.

Reproducible molecular networking of untargeted mass spectrometry data using GNPS

Global Natural Product Social Molecular Networking (GNPS) is an interactive online small molecule-focused tandem mass spectrometry (MS2) data curation and analysis infrastructure. It is intended to provide as much chemical insight as possible into an untargeted MS2 dataset and to connect this chemical insight to the user's underlying biological questions. This can be performed within one liquid chromatography (LC)-MS2 experiment or at the repository scale. GNPS-MassIVE is a public data repository for untargeted MS2 data with sample information (metadata) and annotated MS2 spectra. These publicly accessible data can be annotated and updated with the GNPS infrastructure keeping a continuous record of all changes. This knowledge is disseminated across all public data; it is a living dataset. Molecular networking-one of the main analysis tools used within the GNPS platform-creates a structured data table that reflects the molecular diversity captured in tandem mass spectrometry experiments by computing the relationships of the MS2 spectra as spectral similarity. This protocol provides step-by-step instructions for creating reproducible, high-quality molecular networks. For training purposes, the reader is led through a 90- to 120-min procedure that starts by recalling an example public dataset and its sample information and proceeds to creating and interpreting a molecular network. Each data analysis job can be shared or cloned to disseminate the knowledge gained, thus propagating information that can lead to the discovery of molecules, metabolic pathways, and ecosystem/community interactions.

Implications of indoor microbial ecology and evolution on antibiotic resistance

The indoor environment is an important source of microbial exposures for its human occupants. While we naturally want to favor positive health outcomes, built environment design and operation may counter-intuitively favor negative health outcomes, particularly with regard to antibiotic resistance. Indoor environments contain microbes from both human and non-human origins, providing a unique venue for microbial interactions, including horizontal gene transfer. Furthermore, stressors present in the built environment could favor the exchange of genetic material in general and the retention of antibiotic resistance genes in particular. Intrinsic and acquired antibiotic resistance both pose a potential threat to human health; these phenomena need to be considered and controlled separately. The presence of both environmental and human-associated microbes, along with their associated antibiotic resistance genes, in the face of stressors, including antimicrobial chemicals, creates a unique opportunity for the undesirable spread of antibiotic resistance. In this review, we summarize studies and findings related to various interactions between human-associated bacteria, environmental bacteria, and built environment conditions, and particularly their relation to antibiotic resistance, aiming to guide "healthy" building design.

Characterizing sources and emissions of volatile organic compounds in a northern California residence using space- and time-resolved measurements

We investigate source characteristics and emission dynamics of volatile organic compounds (VOCs) in a single-family house in California utilizing time- and space-resolved measurements. About 200 VOC signals, corresponding to more than 200 species, were measured during 8 weeks in summer and five in winter. Spatially resolved measurements, along with tracer data, reveal that VOCs in the living space were mainly emitted directly into that space, with minor contributions from the crawlspace, attic, or outdoors. Time-resolved measurements in the living space exhibited baseline levels far above outdoor levels for most VOCs; many compounds also displayed patterns of intermittent short-term enhancements (spikes) well above the indoor baseline. Compounds were categorized as "high-baseline" or "spike-dominated" based on indoor-to-outdoor concentration ratio and indoor mean-to-median ratio. Short-term spikes were associated with occupants and their activities, especially cooking. High-baseline compounds indicate continuous indoor emissions from building materials and furnishings. Indoor emission rates for high-baseline species, quantified with 2-hour resolution, exhibited strong temperature dependence and were affected by air-change rates. Decomposition of wooden building materials is suggested as a major source for acetic acid, formic acid, and methanol, which together accounted for ~75% of the total continuous indoor emissions of high-baseline species.

Impacts of indoor surface finishes on bacterial viability

Microbes in indoor environments are constantly being exposed to antimicrobial surface finishes. Many are rendered non-viable after spending extended periods of time under low-moisture, low-nutrient surface conditions, regardless of whether those surfaces have been amended with antimicrobial chemicals. However, some microorganisms remain viable even after prolonged exposure to these hostile conditions. Work with specific model pathogens makes it difficult to draw general conclusions about how chemical and physical properties of surfaces affect microbes. Here, we explore the survival of a synthetic community of non-model microorganisms isolated from built environments following exposure to three chemically and physically distinct surface finishes. Our findings demonstrated the differences in bacterial survival associated with three chemically and physically distinct materials. Alkaline clay surfaces select for an alkaliphilic bacterium, Kocuria rosea, whereas acidic mold-resistant paint favors Bacillus timonensis, a Gram-negative spore-forming bacterium that also survives on antimicrobial surfaces after 24 hours of exposure. Additionally, antibiotic-resistant Pantoea allii did not exhibit prolonged retention on antimicrobial surfaces. Our controlled microcosm experiment integrates measurement of indoor chemistry and microbiology to elucidate the complex biochemical interactions that influence the indoor microbiome.

A different suite: The assemblage of distinct fungal communities in water-damaged units of a poorly-maintained public housing building

Water-damaged housing has been associated with a number of negative health outcomes, principally respiratory disease and asthma. Much of what we know about fungi associated with water-damaged buildings has come from culture-based and immunochemical methods. Few studies have used high-throughput sequencing technologies to assess the impact of water-damage on microbial communities in residential buildings. In this study we used amplicon sequencing and quantitative-PCR to evaluate fungal communities on surfaces and in airborne dust in multiple units of a condemned public housing project located in the San Francisco Bay Area. We recruited 21 households to participate in this study and characterized their apartments as either a unit with visible mold or no visible mold. We sampled airborne fungi from dust settled over a month-long time period from the outdoors, in units with no visible mold, and units with visible mold. In units with visible mold we additionally sampled the visible fungal colonies from bathrooms, kitchens, bedrooms, and living rooms. We found that fungal biomass in settled dust was greater outdoors compared to indoors, but there was no significant difference of fungal biomass in units with visible mold and no visible mold. Interestingly, we found that fungal diversity was reduced in units with visible mold compared to units with no visible mold and the outdoors. Units with visible mold harbored fungal communities distinct from units with no visible mold and the outdoors. Units with visible mold had a greater abundance of taxa within the classes Eurotiomycetes, Saccharomycetes, and Wallemiomycetes. Colonies of fungi collected from units with visible mold were dominated by two Cladosporium species, C. sphaerospermum and C halotolerans. This study demonstrates that high-throughput sequencing of fungi indoors can be a useful strategy for distinguishing distinct microbial exposures in water-damaged homes with visible and nonvisible mold growth, and may provide a microbial means for identifying water damaged housing.

Precision public health to inhibit the contagion of disease and move toward a future in which microbes spread health

Antimicrobial resistance continues to outpace the development of new chemotherapeutics. Novel pathogens continue to evolve and emerge. Public health innovation has the potential to open a new front in the war of "our wits against their genes" (Joshua Lederberg). Dense sampling coupled to next generation sequencing can increase the spatial and temporal resolution of microbial characterization while sensor technologies precisely map physical parameters relevant to microbial survival and spread. Microbial, physical, and epidemiological big data could be combined to improve prospective risk identification. However, applied in the wrong way, these approaches may not realize their maximum potential benefits and could even do harm. Minimizing microbial-human interactions would be a mistake. There is evidence that microbes previously thought of at best "benign" may actually enhance human health. Benign and health-promoting microbiomes may, or may not, spread via mechanisms similar to pathogens. Infectious vaccines are approaching readiness to make enhanced contributions to herd immunity. The rigorously defined nature of infectious vaccines contrasts with indigenous "benign or health-promoting microbiomes" but they may converge. A "microbial Neolithic revolution" is a possible future in which human microbial-associations are understood and managed analogously to the macro-agriculture of plants and animals. Tradeoffs need to be framed in order to understand health-promoting potentials of benign, and/or health-promoting microbiomes and infectious vaccines while also discouraging pathogens. Super-spreaders are currently defined as individuals who play an outsized role in the contagion of infectious disease. A key unanswered question is whether the super-spreader concept may apply similarly to health-promoting microbes. The complex interactions of individual rights, community health, pathogen contagion, the spread of benign, and of health-promoting microbiomes including infectious vaccines require study. Advancing the detailed understanding of heterogeneity in microbial spread is very likely to yield important insights relevant to public health.

Microwave detection and quantification of water hidden in and on building materials: implications for healthy buildings and microbiome studies

BACKGROUND

Excess water in all its forms (moisture, dampness, hidden water) in buildings negatively impacts occupant health but is hard to reliably detect and quantify. Recent advances in through-wall imaging recommend microwaves as a tool with a high potential to noninvasively detect and quantify water throughout buildings.

METHODS

Microwaves in both transmission and reflection (radar) modes were used to perform a simple demonstration of the detection of water both on and hidden within building materials.

RESULTS

We used both transmission and reflection modes to detect as little as 1 mL of water between two 7 cm thicknesses of concrete. The reflection mode was also used to detect 1 mL of water on a metal surface. We observed oscillations in transmitted and reflected microwave amplitude as a function of microwave wavelength and water layer thickness, which we attribute to thin-film interference effects.

CONCLUSIONS

Improving the detection of water in buildings could help design, maintenance, and remediation become more efficient and effective and perhaps increase the value of microbiome sequence data. Microwave characterization of all forms of water throughout buildings is possible; its practical development would require new collaborations among microwave physicists or engineers, architects, building engineers, remediation practitioners, epidemiologists, and microbiologists.

Microbial Exchange via Fomites and Implications for Human Health

PURPOSE OF REVIEW

Fomites are inanimate objects that become colonized with microbes and serve as potential intermediaries for transmission to/from humans. This review summarizes recent literature on fomite contamination and microbial survival in the built environment, transmission between fomites and humans, and implications for human health.

RECENT FINDINGS

Applications of molecular sequencing techniques to analyze microbial samples have increased our understanding of the microbial diversity that exists in the built environment. This growing body of research has established that microbial communities on surfaces include substantial diversity, with considerable dynamics. While many microbial taxa likely die or lay dormant, some organisms survive, including those that are potentially beneficial, benign, or pathogenic. Surface characteristics also influence microbial survival and rates of transfer to and from humans. Recent research has combined experimental data, mechanistic modeling, and epidemiological approaches to shed light on the likely contributors to microbial exchange between fomites and humans and their contributions to adverse (and even potentially beneficial) human health outcomes.

SUMMARY

In addition to concerns for fomite transmission of potential pathogens, new analytical tools have uncovered other microbial matters that can be transmitted indirectly via fomites, including entire microbial communities and antibiotic-resistant bacteria. Mathematical models and epidemiological approaches can provide insight on human health implications. However, both are subject to limitations associated with study design, and there is a need to better understand appropriate input model parameters. Fomites remain an important mechanism of transmission of many microbes, along with direct contact and short- and long-range aerosols.

Modeling the formation and growth of organic films on indoor surfaces

Emission, transport, and fate of semi-volatile organic compounds (SVOCs), which include plasticizers, flame retardants, pesticides, biocides, and oxidation products of volatile organic compounds, are influenced in part by their tendency to sorb to indoor surfaces. A thin organic film enhances this effect, because it acts as both an SVOC sink and a source, thus potentially prolonging human exposure. Unfortunately, our ability to describe the initial formation and subsequent growth of organic films on indoor surfaces is limited. To overcome this gap, we propose a mass transfer model accounting for adsorption, condensation, and absorption of multiple gas-phase SVOCs on impervious, vertical indoor surfaces. Further model development and experimental research are needed including more realistic scenarios accounting for surface heterogeneity, non-ideal organic mixtures, and particle deposition.

Daylight exposure modulates bacterial communities associated with household dust

BACKGROUND

Microbial communities associated with indoor dust abound in the built environment. The transmission of sunlight through windows is a key building design consideration, but the effects of light exposure on dust communities remain unclear. We report results of an experiment and computational models designed to assess the effects of light exposure and wavelengths on the structure of the dust microbiome. Specifically, we placed household dust in replicate model "rooms" with windows that transmitted visible, ultraviolet, or no light and measured taxonomic compositions, absolute abundances, and viabilities of the resulting bacterial communities.

RESULTS

Light exposure per se led to lower abundances of viable bacteria and communities that were compositionally distinct from dark rooms, suggesting preferential inactivation of some microbes over others under daylighting conditions. Differences between communities experiencing visible and ultraviolet light wavelengths were relatively minor, manifesting primarily in abundances of dead human-derived taxa. Daylighting was associated with the loss of a few numerically dominant groups of related microorganisms and apparent increases in the abundances of some rare groups, suggesting that a small number of microorganisms may have exhibited modest population growth under lighting conditions. Although biological processes like population growth on dust could have generated these patterns, we also present an alternate statistical explanation using sampling models from ecology; simulations indicate that artefactual, apparent increases in the abundances of very rare taxa may be a null expectation following the selective inactivation of dominant microorganisms in a community.

CONCLUSIONS

Our experimental and simulation-based results indicate that dust contains living bacterial taxa that can be inactivated following changes in local abiotic conditions and suggest that the bactericidal potential of ordinary window-filtered sunlight may be similar to ultraviolet wavelengths across dosages that are relevant to real buildings.

Leaves of Indoor Ornamentals Are Biodiversity and Functional Hotspots for Fungi

Leaf-inhabiting fungi are an important, but often overlooked component of molecular biodiversity studies. To understand their diversity and function in relation to plant species and climate, the phyllospheres of 14 phylogenetically diverse ornamental plant species were analyzed under different controlled greenhouse conditions. We found unexpectedly high fungal diversity (H' = 2.8-6.5), OTU numbers (449-1050) and abundances (103-106 CFU cm-2 leaf surface) associated with all plants studied indoors. Despite experimental limitations, the composition of fungal communities were inclined toward a plant species-dependent pattern compared to the ambient climatic variables. Most detected fungi were patho- and saprotrophs showing a yeast-like growth morphology and were associated to the groups of endophytes and potential plant pathogens in a plant species-specific manner. A representative strain collection showed that 1/3 of the tested fungi (mainly Penicillium, Cladosporium, and Cryptococcus spp.) were able to inhibit mycelial growth and 2/3 inhibit sporulation of the plant pathogen Botrytis cinerea by the production of antifungal volatile organic compounds (VOCs) completely. This study indicates that plant leaves harbor a stable phyllosphere fungal diversity in diverse microclimates and enrich distinctive functional guilds.

Emission Factors of Microbial Volatile Organic Compounds from Environmental Bacteria and Fungi

Knowledge of the factors controlling the diverse chemical emissions of common environmental bacteria and fungi is crucial because they are important signal molecules for these microbes that also could influence humans. We show here not only a high diversity of mVOCs but that their abundance can differ greatly in different environmental contexts. Microbial volatiles exhibit dynamic changes across microbial growth phases, resulting in variance of composition and emission rate of species-specific and generic mVOCs. In vitro experiments documented emissions of a wide range of mVOCs (>400 different chemicals) at high time resolution from diverse microbial species grown under different controlled conditions on nutrient media, or residential structural materials ( N = 54, N_control = 23). Emissions of mVOCs varied not only between microbial taxa at a given condition but also as a function of life stage and substrate type. We quantify emission factors for total and specific mVOCs normalized for respiration rates to account for the microbial activity during their stationary phase. Our VOC measurements of different microbial taxa indicate that a variety of factors beyond temperature and water activity, such as substrate type, microbial symbiosis, growth phase, and lifecycle affect the magnitude and composition of mVOC emission.

Fluorescent biological aerosol particles: Concentrations, emissions, and exposures in a northern California residence

Residences represent an important site for bioaerosol exposure. We studied bioaerosol concentrations, emissions, and exposures in a single-family residence in northern California with 2 occupants using real-time instrumentation during 2 monitoring campaigns (8 weeks during August-October 2016 and 5 weeks during January-March 2017). Time- and size-resolved fluorescent biological aerosol particles (FBAP) and total airborne particles were measured in real time in the kitchen using an ultraviolet aerodynamic particle sizer (UVAPS). Time-resolved occupancy status, household activity data, air-change rates, and spatial distribution of size-resolved particles were also determined throughout the house. Occupant activities strongly influenced indoor FBAP levels. Indoor FBAP concentrations were an order of magnitude higher when the house was occupied than when the house was vacant. Applying an integral material-balance approach, geometric mean of total FBAP emissions from human activities observed to perturb indoor levels were in the range of 10-50 million particles per event. During the summer and winter campaigns, occupants spent an average of 10 and 8.5 hours per day, respectively, awake and at home. During these hours, the geometric mean daily-averaged FBAP exposure concentration (1-10 μm diameter) was similar for each subject at 40 particles/L for summer and 29 particles/L for winter.

Indoor Chemistry

This review aims to encapsulate the importance, ubiquity, and complexity of indoor chemistry. We discuss the many sources of indoor air pollutants and summarize their chemical reactions in the air and on surfaces. We also summarize some of the known impacts of human occupants, who act as sources and sinks of indoor chemicals, and whose activities (e.g., cooking, cleaning, smoking) can lead to extremely high pollutant concentrations. As we begin to use increasingly sensitive and selective instrumentation indoors, we are learning more about chemistry in this relatively understudied environment.