Claudia K. Gunsch

Built structures host complex and dynamic microbial communities whose assembly is shaped by occupancy, ventilation, building materials, cleaning practices, connections to outdoor environments, and other factors. These communities, collectively described as the microbiome of the built environment (MoBE), are increasingly recognized as critical to human health, yet there is currently no consensus definition of what constitutes a healthy MoBE. This gap impedes the development of engineering efforts to balance microbial diversity and immune support with the minimization of infectious disease risks. We propose three pillars that together define a healthy MoBE: (i) pathogens below context-specific risk thresholds; (ii) non-sterility, as sterility is likely to be suboptimal for human health in most contexts; and (iii) resilient diversity, as more diverse communities may resist pathogen colonization and recover more rapidly from perturbations. We synthesize evidence for each pillar, propose a framework for feedback-controlled MoBE engineering, and discuss how pillar priorities should be weighted across building types and occupant populations. We identify critical research priorities to advance actionable performance standards in support of healthy buildings.

Background: Built environments function as hubs of microbial exchange, and kitchens serve as key sites for interaction between occupants and physical surfaces. Understanding how spatial connectivity and regional variation influence bacterial and fungal colonization on kitchen surfaces is relevant to the protection of human health and food safety. Here, we applied long-read 16S rRNA and ITS amplicon sequencing to samples collected from countertops, drain holes, and faucet spouts (n = 123) in 41 residential kitchens across two counties in North Carolina, USA to quantify variation in microbial community structure across multiple spatial scales. Results: We found lower taxonomic resolution for bacteria than for fungi, with species-level assignments representing ~ 30% of bacterial reads and ~ 88% of fungal reads. Community structure was driven primarily by kitchen identity (45% of bacterial and 37% of fungal variation), with ZIP code, surface type and county each explaining smaller, yet significant, proportions of the observed variation. Countertops exhibited the highest bacterial and fungal diversity, whereas drain holes and faucet spouts were dominated by taxa including Pseudomonas , Acinetobacter , Penicillium , and Candida . Targeted taxonomic screening identified Stenotrophomonas maltophilia , Acinetobacter junii , Aspergillus fumigatus , and Penicillium brevicompactum , indicating that sink surfaces can harbor opportunistic taxa associated with infections in immunocompromised individuals. Conclusions: Our findings demonstrate that kitchen identity signatures dominate microbial community structure, with moisture-retaining surfaces acting as key niches. This multi-scale structuring supports the framework that indoor microbiomes are seeded by outdoor inputs but structured by human occupancy.

Polycyclic aromatic hydrocarbons (PAHs) are hazardous organic contaminants for which microbial bioaugmentation is a promising remediation strategy, but poor persistence of introduced microorganisms can limit efficacy. Encapsulation may improve persistence, yet the influence of capsule design, microbial species, and environmental conditions on performance remains poorly understood. We evaluated alginate encapsulation of the PAH-degrading bacteria Pseudomonas putida and Novosphingobium aromaticivorans across nutrient conditions and capsule formulations. Encapsulation effects varied by species and medium, influencing growth rate, maximum cell density, overall growth, and lag time; notably, encapsulation shortened lag time of N. aromaticivorans in sRB ₁₅ medium (36.9 h to 3.9-5.3 h). Enumeration methods also affected apparent cell recovery. After 8 weeks, encapsulation had no significant effect on P. putida but resulted in increased concentrations of N. aromaticivorans relative to planktonic cultures (1.22 x 10 ⁸ CFU/mL vs. 2.05 x 10 ⁶ CFU/mL). Capsule composition further influenced cell retention: increasing alginate approximately doubled capsule-associated cell concentrations, while chitosan coatings reduced cell concentrations within capsules without affecting external concentrations. These findings demonstrate that the benefits of encapsulation are species- and environment-dependent and that capsule formulation can be tuned to influence bacterial persistence and release, informing the design of encapsulated inoculants for bioaugmentation applications.

Polycyclic aromatic hydrocarbons (PAHs) are persistent, hydrophobic contaminants that accumulate in sediments, where limited bioavailability restricts microbial degradation and hinders bioaugmentation strategies. Encapsulation has emerged as a promising approach to improve microbial establishment during bioaugmentations, yet its influence on contaminant partitioning and degradation dynamics remains poorly understood. In this study, we encapsulated two PAH degrading fungal isolates, Trichodermadeliquescens and Aureobasidium sp., in sodium alginate hydrogels and evaluated fungal growth, long term viability, and PAH removal in controlled laboratory systems. Encapsulation consistently shortened fungal lag phases, suggesting more rapid establishment following inoculation. Over an eight-week period, encapsulated T. deliquescens maintained stable viability, whereas free-living cultures declined by approximately 1.4 log CFU (p < 0.01). In contrast, encapsulation had little effect on the long-term viability of yeast like Aureobasidium, indicating that the benefits of encapsulation depend on fungal morphology. While free living cultures generally exhibited greater apparent removal of phenanthrene and fluoranthene, mass balance analyses revealed that alginate capsules accumulated substantial quantities of PAHs (50-150ng mL-1), with sorption increasing as compound hydrophobicity increased. This finding identifies alginate as an underrecognized sink for nonpolar contaminants that alters apparent degradation kinetics by modifying contaminant partitioning rather than inhibiting fungal activity. These results demonstrate that encapsulation influences bioaugmentation through two complementary mechanisms: enhancing the establishment of select fungal species while simultaneously altering contaminant bioavailability and mass transfer. These findings provide new mechanistic insight into encapsulated bioremediation systems and highlight the importance of accounting for contaminant sorption when designing and interpreting encapsulation based bioaugmentation strategies.

Microbiome Engineering of the Built Environment (MEoBE) is an emerging field with the potential to improve public health through the introduction or preservation of beneficial microbiomes and the r...

Here, we report the draft genome sequences of Trichoderma deliquescens and Aureobasidium sp., fungi isolated from sediments of the Elizabeth River. Genomes assembled from Nanopore sequencing revealed genes encoding enzymes implicated in polycyclic aromatic hydrocarbon (PAH) degradation. These resources provide genomic insights into fungal PAH degradation and inform bioremediation strategies.

The built environment (BE), where we spend the majority of our time, contains a variety of surfaces with distinct properties. Our understanding of how these surfaces shape the microbiome of the BE (MoBE) is underdeveloped and limits the ability to develop a bioinformed microbial management framework. Lab-scale studies have shown the impact of surface properties (roughness, wettability, porosity) on microbial communities, but studies sampling the BE microbiome have often overlooked this metadata. A keyword search of the literature found that only 31% of studies that sampled the indoor microbiome reported material information, which did not include any material characterization data. We have used the kitchen as a case study to illustrate the complexity of the microbial community and material surfaces that are present in the BE. We also describe how the use of BE spaces, such as cleaning, can impact both the materials and microbial community. We propose an interdisciplinary approach to studying the MoBE, incorporating techniques from material characterization into environmental microbiological sampling to elucidate the role of materials and their surface properties on the MoBE. Utilizing this interdisciplinary approach, a bioinformed framework can be developed for managing healthy MoBEs—one that improves occupant health by incorporating material science into microbial risk assessment and design strategies.

Sink P-traps harbor microbial communities derived from environmental and human sources, yet longitudinal studies examining their stability and assembly dynamics remain limited. Here, we present, to our knowledge, the longest continuous characterization of bacteria collected from residential sink P-traps, with daily sampling over two months (n = 61 days). Samples were collected from paired sinks in a shared bathroom to identify dominant taxa, quantify temporal stability, and determine how occupant usage patterns influence community assembly. Using full-length 16S rRNA gene sequencing, we identified 3,865 unique taxa, with both sinks dominated by common sink-associated genera, including Pseudomonas , Citrobacter , Klebsiella , and Arcobacter . Despite sharing identical plumbing, environmental conditions, and cleaning regimes, the two sinks maintained distinct communities (p < 0.001). Temporal stability analyses revealed notable differences: Sink A (male; hand washing, toothbrushing, shaving) exhibited deterministic dynamics with low variability (CV = 4.9%), significant temporal autocorrelation (p = 0.001), and predictable trajectories, with time explaining 49.9% of community variation. In contrast, Sink B (female; hand washing, toothbrushing, face washing, mouthwash use) displayed stochastic dynamics with high volatility (CV = 26.5%), no significant autocorrelation (p = 0.53), and minimal temporal predictability. Differential abundance analysis revealed that Sink B was enriched in anaerobes, biofilm-forming taxa, oral microbiome associates, and preservative-resistant and lipid-degrading bacteria, while Sink A harbored a more aerobic, skin-associated community. These findings demonstrate that individual usage patterns (particularly exposure to biocidal agents) can alter P-trap community structure and temporal dynamics, with implications for microbial community prediction in residential and healthcare settings. Importance: Sink drains are increasingly recognized as reservoirs for antimicrobial-resistant pathogens, yet we lack fundamental knowledge about what drives bacterial community dynamics in these environments. By sampling paired residential sink P-traps daily for two months, we show that individual-specific behaviors, such as using products with a biocidal effect, can alter community composition from a stable, predictable state to one characterized by stochastic fluctuations. The sink exposed to mouthwash and face wash harbored more anaerobes, biofilm formers, and oral bacteria, suggesting that repeated exposure promotes disturbance-tolerant taxa rather than reducing bacterial colonization. These results provide a baseline ecological framework for understanding P-trap microbiomes and suggest that predictive monitoring of sink-associated pathogens might be feasible in stable environments but more difficult when there is variable antimicrobial exposure -- a finding directly relevant to hospital infection control.

Healthcare Associated Infections (HAIs) pose a significant public health risk. Hospital sinks and associated plumbing are one likely source. This study investigates bioaerosol emissions from sink P-traps during faucet operation to assess their potential role in pathogen transmission in the hospital context. We designed an aerosol chamber system with adjustable air change rate and a functioning sink meeting hospital standards. We quantified bioaerosol and large droplet emission factors from the sink, using FAmpEscherichia coli as a model for Enterobacteriaceae such as Klebsiella pneumoniae. We cultured Andersen Cascade Impactor and BioSpot sampler aerosol samples and deposition plates using MI agar, which is selective for E. coli. Across five experiments, deposition plate counts were substantial, while air samples were close to detection limits. We estimated PM5.0 bioaerosol emissions factors of 1.3 x 10-10 to 1.9 x 10-10 CFU emitted per CFU in P-trap. Large droplet emission factor was one order of magnitude larger, at 4.3 x 10-9 ± 2.8 x 10-9 CFU per CFU. Results were used to predict Klebsiella pneumoniae inhalation dose (0.78 to 1.12 CFU day-1) and inhalation infection probability (∼10-5) for 5.5 day hospital stay with colonized plumbing (air change rate 6 h-1). This translates to ∼1 infection per year for a hospital with a severe plumbing system colonization affecting ∼2000 continuously occupied rooms. For pathogens with different dose response curves, we demonstrate how infection probability via inhalation depends on dose response.