A Comparison of Techniques for Collecting Skin Microbiome Samples: Swabbing Versus Tape-Stripping

Abstract

The swabbing and tape-stripping methods have traditionally been used for collecting skin microbiome samples for skin bacterial analysis, although no reports have compared the outcome of these methods for collecting skin bacteria. Our purpose was to show the differences in microbial composition between samples collected using the swabbing and tape-stripping methods, by both the next generation sequencing and culture studies. The skin microbiome was collected by both methods, and the samples were processed for a sequence-based microbiome analysis and culture study. The next-generation sequencing results showed that skin bacteria collected using the tape-stripping method were comparable to those collected using the swabbing method. In the culture study, the tape-stripping method collected a greater number and wider variety of viable skin bacteria than the swabbing method. These results suggest that the tape-stripping method is comparable to the swabbing method for collecting viable skin bacteria, without losing fidelity to the composition of skin microbiome.

Keywords: bacterial culture; next generation sequencing; skin microbiome; swabbing; tape stripping.

FIGURE 1

Yield of total DNA and 16S rRNA gene. (A) The amount of total DNA collected using the swabbing and tape-stripping methods. (B) The copy number of the 16S rRNA gene obtained by the swabbing and tape-stripping methods. The data points of the swabbing and tape-stripping methods from the same participant are connected.

FIGURE 2

Relative abundance of bacteria classified at the genus level (top 20). Note the high similarity between the swabbing and tape-stripping methods within each participant, indicated by the Yue and Clayton theta index (𝜃_YC) and Pearson’s correlation coefficient (r). Sw, swabbing method; Tp, tape-stripping method.

FIGURE 3

Beta diversity based on the weighted UniFrac distance. Each color denotes each participant. Spheres and cubes indicate the data obtained from the swabbing and tape-stripping methods, respectively. PC, principal coordinate.

FIGURE 4

Rarefaction curves and the comparison of alpha diversity indices between the swabbing and tape-stripping methods. A rarefaction analysis on the number of observed operational taxonomic units (OTUs) (A), phylogenetic diversity (B), Chao1 index (C), and Shannon diversity index (D). The analysis was performed up to 9,840 depth. The colors of each plot were assigned as red for the swabbing method and blue for the tape-stripping method. Each index was compared at the rarefaction depth at 9,840. Sw, swabbing method; Tp, tape-stripping method.

FIGURE 5

The number of colonies in the culture study. The number of colonies cultured under aerobic (A) and anaerobic (B) conditions were counted. The data points of the swabbing and tape-stripping methods from the same participant are connected. ^∗P < 0.05. cfu, colony forming unit.

FIGURE 6

Cultured bacteria using the swabbing and tape-stripping methods confirmed by qualitative PCR. Species-specific primers are as in Supplementary Table 1. Bacterial species in bold are skin commensal bacteria. ^∗B. anthracis, B. thuringiensis, B. mycoides.