A deployable film method to enable replicable sampling of low-abundance environmental microbiomes

Abstract

Urbanizing global populations spend over 90% of their time indoors where microbiome abundance and diversity are low. Chronic exposure to microbiomes with low abundance and diversity have demonstrated negative long-term impacts on human health. Sequencing-based analyses of environmental nucleic acids are critical to understanding the impact of the indoor microbiome on human health, however low DNA yields indoors, alongside sample collection and processing inconsistencies, currently challenge study replicability. This study presents a comparative assessment of a novel, passive, easily replicable sampling strategy using polydimethylsiloxane (PDMS) sheets alongside a representative swab-based collection protocol. Deployable, customizable PDMS films designed for whole-sample insertion into standardized extraction kits demonstrated 43% higher DNA yields per sample, and 76% higher yields per cm² of sampler over swab-based protocols. These results indicate that this accessible, scalable method enables sufficient DNA collection to comprehensively evaluate indoor microbiome exposures and potential human health impacts using smaller, more space efficient samplers, representing an attractive alternative to swab-based collection. In addition, this process reduces the manual steps required for microbiome sampling which could address inter-study variability, transform the current microbiome sampling paradigm, and ultimately benefit the replicability and accessibility of microbiome exposure studies.

Keywords: DNA yield; Extraction efficiency; High-throughput sequencing; Indoor microbiome; PDMS; Passive sampling.

Fig. 1

(A) Illustrating the relative sizes of the eight samplers. White dots represent 1 µL of the diluted microbial community master mix. Samplers are drawn according to scale. Rectangular diagrams represent PDMS samplers in a variety of sizes inserted in their entirety into extraction kit collection tubes. The circular diagram represents a petri dish where collection required swabbing and inserting the swab head into extraction kit collection tubes. (B) Comparing PDMS with swab inputs and relationships to extraction bead-beating tube size constraints. (C) Comparing the field replicability of three samplers from section “A” (boxed) illustrating how the size and shape of each sampler impacts the number of possible sample replicates within a hypothetical deployment area of 400cm2.

Fig. 2

(A) Line range plots of total DNA yield. (B) Line range plots of calculated extraction efficiencies in reference to positive controls (see Methods). Median values of the largest PDMS samplers included within each extraction kit are circled. The lowest quantified extraction efficiencies within each group are denoted. (C) Line range plots of DNA yield per cm2 of sampler area. Average DNA yield per cm2 is denoted for discussed samplers.

Fig. 3

Relative abundance (%) of the non-reference species identified by sampler/extraction kit protocols. A full list and average relative abundance by sampler can be found in Table SIV.

Fig. 4

A metagenomic analysis of the community structure for three representative samplers (Figure 1A&C). Outcomes were compared to the provided mock community reference numbers “R” (Bray–Curtis Dissimilarity), and species-level outcomes were compared within PDMS/Swab sampler groups (Kruskal–Wallis).

Fig. 5

An example of the 117cm2 PDMS deployable film in triplicate within an indoor office space.